Production of anti-self antibodies from antibody segment repertoires and displayed on phage

ABSTRACT

Methods are disclosed for the production of anti-self antibodies and antibody fragments, being antibodies or fragments of a particular species of mammal which bind self antigens of that species. Methods comprise providing a library of replicable genetic display packages (rgdps), such as filamentous phage, each rgdp displaying at its surface member of a specific binding pair which is an antibody or antibody fragment, and each rgdp containing nucleic acid sequence derived from a species of mammal. The nucleic acid sequence in each rgdp encodes a polypeptide chain which is a component part of the sbp member displayed at the surface of that rgdp. Anti-self antibody fragments are selected by binding with a self antigen from said species of mammal. The displayed antibody fragments may be scFv, Fd, Fab or any other fragment which has the capability of binding antigen. Nucleic acid libraries used may be derived from rearranged V-gene sequences of unimmunised mammal. Synthetic or artificial libraries are described and shown to be useful.

This is a continuation of co-pending U.S. application Ser. No.10/326,495 filed Dec. 19, 2002 (allowed) which is a continuation of U.S.application Ser. No. 09/197,224, filed Nov. 20, 1998, now U.S. Pat. No.6,521,404, which is a continuation of U.S. application Ser. No.08/244,597, filed Dec. 2, 1992, now U.S. Pat. No. 5,885,793, which inturn is a U.S. National phase of PCT/GB92/02240, filed Dec. 2, 1992,which claims priority to GB 9125579.4 filed Dec. 2, 1991, GB 9125582.8filed Dec. 2, 1991, GB 9206318.9 filed Mar. 24, 1992, GB 9206372.6 filedMar. 24, 1992 and PCT/GB92/01755 filed Sep. 23, 1992. Each of theforegoing applications is hereby incorporated by reference herein.

This invention relates to the isolation of antibody molecules directedagainst self antigens, e.g. human antibodies directed against human selfantigens. Phage display technology for selection of antibody moleculeswas described-in WO92/01047, PCT/GB92/00883, PCT/GB92/01755 andGB9206372.6. The applicants have realised that antibodies directedagainst self antigens can be isolated using phage display technology.

Human antiself antibodies are of particular value for in vivotherapeutic and diagnostic purposes, since they avoid the problemsarising from the antigenicity of foreign, e.g. mouse antibodies. Themost useful human antibodies for therapy are those directed against cellsurface molecules, such as receptors, adhesins and integrins, and thosedirected against circulating biological effector molecules, such ashormones, growth factors and cytokines. It has been extremely difficultto obtain human antibodies against such self antigens. This inventionprovides a powerful way of obtaining such antibodies.

It is a demanding task to isolate an antibody fragment with specificityagainst self antigen. Animals do not normally produce antibodies to selfantigens, a phenomenon called tolerance (G. J. Nossal Science 245147-153, 1989). Autoimmune diseases may result from a breakdown intolerance. In general, vaccination with a self antigen does not resultin production of circulating antibodies. It is therefore difficult toraise antibodies to self antigens, particularly in humans. It ispossible to raise antibodies that recognise human antigens in an animalsuch as a mouse, especially if the human antigen is not too closelyrelated to any equivalent in the animal. If a human antibody is thenrequired it is necessary to ‘humanise’ the antibody, e.g. by CDRgrafting (patent GB2188638B).

Phage antibody technology as described in (WO92/01047) offers theability to isolate such human antibodies directly in this application,we demonstrate for the first time that antibodies against self-antigenscan be isolated from phage libraries derived from, for example,nonimmunised sources and from libraries prepared by syntheticrecombination of V-gene sequences, preferably recombination of VH with,DH and JH, and VL with JL sequences. These antibodies are specific fortheir antigen. This application shows that single libraries derived inthis manner can act as a source of both foreign and self antigens andopens up the prospect of a large, universal library to isolateantibodies to any antigen.

It was disclosed in patent application WO92/01047 that antibodyfragments can be displayed on the surface of bacteriophage and that theywill bind antigen. Antibody fragments can be directly selected usingthis characteristic. This ability to isolate antibody fragments (Fab,Fv, scvF, and VH) using their display on the surface of filamentousbacteriophage has opened up the prospect of the isolation of antibodyspecificities (i.e. antibodies directed against a particular antigen)that were difficult or impossible to isolate previously. In particularWO92/01047 demonstrates that antibody specificities can be isolated froma human who has not been specifically immunised (‘unimmunised’), evenspecificities for antigens such as 2-phenyl-5-oxazolone to which humanswill not normally be exposed.

In embodiments of this invention, natural or synthetic antibodyrepertoires derived from a species of mammal, such as human, mouse, rat,sheep, pig, goat, horse or other, are displayed on the surface of areplicable genetic display package (rgdp) and the binding specificityfor self is selected by binding to self antigen. In this process, the Vgene repertoires are derived from V genes rearranged in vitro or in vivoand or by mutation of (a) rearranged V gene(s). A key feature of the Vgene repertoires is that they are extremely diverse in sequence, usuallyin excess of 10⁶ different members. Indeed it is possible that asufficiently large library may provide a source of specificitiesdirected against any self antigen. The V-gene repertoires are clonedinto the rgdp (for example a filamentous phage vector) such thatantibody repertoires are displayed on the surface of the rgdp. The rgdpsencoding rare antibody specificities binding to antiself, may beselected by virtue of binding to the self antigen. The antibodyrepertoires may be cloned in a single replicon or a dual replicon formatas described in WO92/01047 and PCT/GB92/00883.

The V genes may be cloned into the genetic material of the rgdp, andexpressed as single domains, for example single heavy chain variabledomains, so called single domain ligands or “dAbs” (see WO90/01544), oras associated antibody heavy and light chain variable domains.

The two domains could be displayed as separate polypeptide chains(linked as in Fab fragments through non-covalent association of domainsand/or disulphide bonds), or as part of the same chain (single chain Fvfragments where the two domains are contained within the samepolypeptide chain).

In WO92/01047 and examples 1 to 8 of this application we have usedfusion of antibody fragments to gene 3 protein of filamentousbacteriophage for display and selection of antibody fragments. Analternative approach would be to fuse antibody fragments to gene 8protein or other surface molecules of filamentous bacteriophage.

Isolation of human antibodies directed against human antigens is ademanding task. There are only a limited number of human antigensagainst which circulating human antibodies are naturally found.Antibodies are present directed against non-self antigens of humanorigin. Antibodies directed against human blood group B have beenisolated from a phage display library prepared from subjects of bloodgroup O (J. D. Marks et al, J. Mol. Biol. 222 581-597, 1991), whichrecognise the blood group B antigen as foreign.

This invention is concerned with a general method for the isolation ofantibodies directed against self antigens which are specific for theantigen concerned. Many patients show significant concentrations ofcirculating autoantibodies. It is estimated that 10 to 30% of Blymphocytes in normal, healthy individuals are engaged in makingautoantibodies (I. R. Cohen and A. Cooke Immunol. Today 7 363-364,1986). However, the ‘natural autoantibodies’ produced do not lendthemselves to therapeutic use as they are often IgM, low affinity andpolyreactive (P. Casali and A. L. Notkins Ann. Rev. Immunol. 7 515-531,1989; S. Avrameas Immunol. Today 12 154-159). An immune response againstself can arise in autoimmune disease or after infections and a fewmonoclonal antibodies directed against self antigens have been isolatedfrom patients with autoimmune disease (K. James & G. T. Bell J. Immunol.Methods 100 5-40, 1987). These autoantibodies are frequently specific,but may bind to only a limited range of epitopes on the antigen (M.Bouanani et al Arthritis Rheum. 34 1585-1593, 1991).

The preparation of V gene libraries derived from the mRNA of plasmacells secreting IgG (or IgM) antibody may thus lead to the isolation ofantibody fragments derived from autoantibodies. For instance, anti-selfantibodies might be isolated from patients with autoimmune diseases, forexample anti-acetylcholine receptor antibodies would be expected to beisolated from antibody repertoires made from the IgG mRNA of myastheniagravis patients. For example, an antibody fragment specific for humanthyroid peroxidase has been isolated from a bacteriophage lambda libraryfrom a patient with thyroid autoimmune disease (S. Portolano et alBiochem. Biophys. Res. Commun. 179 372-377, 1991). This however requiredextensive screening of 200,000 plaques to obtain one clone. In addition,this library was derived from thyroid tissue, a procedure not readilyapplicable in-most instances.

In contrast, the power of selection available using the phage system,demonstrated in WO92/01047 allows the ready isolation of autoantibodiesfrom the IgM mRNA of peripheral blood lymphocytes of a donor withoutdisease. We show in example 2 that antibodies binding to humanthyroglobulin (which can be found in the sera of people with or withoutsymptomatic autoimmune disease), can be isolated from phage repertoiresprepared from unimmunised humans. One would not expect necessarily to beable to obtain antibodies to human thyroglobulin by immunising a humanwith human thyroglobulin, notwithstanding the presence of thyroglobulinautoantibodies in many people. Autoantibodies against thyroglobulin innormal sera have been reported often to have a high degree ofpolyreactivity (S. Avrameas, 1991 supra). In contrast, those which areisolated using a method according to the present invention involvingphage antibody technology, see example 2 for instance, are specific forthyroglobulin.

In this application, we also demonstrate that even antibodies againsthuman tumour necrosis factor-α can be isolated as described in example 1from the same library as the antibodies directed against thyroglobulin.Many self antigens do not have detectable associated circulatingautoantibodies. Further, example 3 shows the isolation of antibodiesagainst the self antigens mucin, carcinoembryonic antigen (CEA) and CD4,antibodies to which have not been reported in normal sera. Moreover,these antibodies are specific, whereas there is often a high degree ofpolyreactivity in natural autoantibodies which can sometimes be found.The vast majority of self antigens do not have detectable associatedcirculating autoantibodies. Thus the isolation of antiself antibodies asdescribed in this invention opens the prospect of the direct isolationof human antibodies binding to human antigens for a number of purposessuch as antibodies which bind to circulating hormones to block, modifyor potentiate their action or antibodies that bind to cell surfaceantigen for imaging or killing for example of cancer cells.

The origin of the V genes that contribute to anti-self antibodiesisolated from phage display libraries is not clear. Tolerance to selfantigens by the immune system (preventing the generation of antibodiesdirected against them) is mediated by either clonal deletion orfunctional inactivation (anergy) of self-reactive B lymphocytes (D. A.Nemazee & K. Burki Nature 337 562-566, 1989; C. C. Goodnow et al Nature334 676-682, 1988; S. B. Hartley et al Nature 353 765-769, 1991; D. M.Russell et al Nature 354 308-311, 1991). In either case littlecirculating anti-self antibody is detectable for most antigens. However,in the case of anergy, functionally inactivated self-reactive cells fromthe B cell lineage persist in peripheral lymphoid organs leading to Bcells in circulation. These rare lymphocytes with anti-self specificitymay provide heavy or light chain partners (or even both) for phageantibodies with anti-self specificities. Alternatively, such anti-selfspecificities may arise from the combination in the library of a VHdomain with a VL domain to give a specificity that is normally deletedif it occurs in nature. For this reason, combinatorial libraries and‘chain-shuffled’ libraries such as described in patent applicationsWO92/01047 may be a particularly rich source of anti-self antibodies. Aselection procedure of great power, such as that provided by phageantibodies, is required to obtain such rare anti-self antibodies.

The degree of somatic mutation observed in antiself antibody fragmentsisolated by phage technology in this application indicates that somehave germ line sequences and have therefore arisen from virgin B cells.Other antibodies isolated by phage antibody technology in thisapplication show somatic hypermutation indicating that the V genes havebeen stimulated by antigen, either a foreign cross reactive antigen orother foreign antigens. In both cases the antibody fragments isolatedusing phage technology will usually be a combination of VH and VLdomains not originally present in the B lymphocytes and the power ofphage technology, as described in this application enables theirisolation.

According to the present invention there is provided a method ofobtaining a member of a specific binding pair (sbp member), which sbpmember has an antigen binding site with binding specificity for anantigen which is a self antigen of a species of mammal, the methodcomprising:

-   -   (a) providing a library of replicable genetic display packages        (rgdps), each rgdp displaying at its surface an sbp member, and        each rgdp containing nucleic acid with sequence derived from        said species of mammal and encoding a polypeptide chain which is        a component part of the sbp member displayed at the surface of        that rgdp;    -   (b) selecting, by binding with said self antigen, one or more        sbp members with binding specificity for said self antigen.

The polypeptide component part encoded by the nucleic acid in each rgdpmay be a VH or VL domain of an antibody, or any part of an antibodywhich, either alone or in combination with one or more other componentparts, forms an antibody fragment which is capable of binding anantigen. Examples of polypeptide chains which may be used as componentparts of an sbp member as described above therefore include, in additionto VH and VL domains, V_(L)C_(L), V_(H)C_(H)1, scFv fragments, Fabfragments and so on.

Each said sbp member displayed at the surface of an rgdp may be anantibody fragment comprising a V_(H) domain and a V_(L) domain.

Each antibody fragment may be a scFv fragment, a Fab fragment, a Fvfragment consisting of the V_(L) and V_(H) domain of a single arm of anantibody, a single domain binding ligand consisting essentially of orcomprising a heavy-chain variable domain (Fd), or any other fragmentwhich has the capability of binding an epitope or antigen.

The step of providing a library of rgdps may comprise:

-   -   combining (i) a first polypeptide chain component part of an sbp        member fused to a component of a rgdp which thereby displays        said first polypeptide chain component part or population        thereof at the surface of rgdps on expression in a recombinant        host cell organism, or a population of such a first polypeptide        chain component part fused to a said component of a rgdp,        with (ii) a second polypeptide chain component part of an sbp        member or a population of such a second polypeptide chain        component part, to form a library of sbp members displayed at        the surface of rgdps;    -   at least one of said first or second polypeptide chain component        part or populations thereof being encoded by nucleic acid which        is capable of being packaged using said component of an rgdp.

The step of providing a library of rgdp may comprise:

-   -   expressing in a recombinant host organism a first polypeptide        chain component part of an sbp member or a population of such a        first polypeptide chain component part, fused to a component of        an rgdp which thereby displays said polypeptide chain component        part at the surface of rgdps;    -   combining said first polypeptide chain component part or        population with a second polypeptide chain component part of an        sbp member or a population of such a second polypeptide chain        component part, to form a library of rgdps each displaying an        sbp member at its surface, at least one of said polypeptide        chain component parts being expressed from nucleic acid which is        capable of being packaged using said component of an rgdp.

Where the sbp member is an Fab fragment the first and second polypeptidechain component part may be a polypeptide consisting of a V_(L) and aC_(L) domain, and the second polypeptide chain component part apolypeptide consisting of a V_(H) and a C_(H)1 domain.

The combining of first and second polypeptide chain component parts orpopulations thereof may be at the nucleic acid level with expressionvectors each having introduced therein a sequence encoding a firstcomponent part and a sequence encoding a sequence component part. On theother hand, the combining may be at the polypeptide level with firstcomponent parts not being expressed from the same vectors as secondcomponent parts. Indeed, one or other of the first and second componentparts may be provided as a soluble library. Details of various formatswhich may be employed are given in WO92/01047 and PCT/GB92/00883.

The step of providing a library may comprise:

-   -   combining (i) nucleic acid which encodes a first polypeptide        chain component of an sbp member fused to a component of a rgdp        or a population of such a first polypeptide chain component part        fused to a component of a rgdp, with (ii) nucleic acid encoding        a second polypeptide chain component part of an sbp member or a        population thereof, to form a library of nucleic acid, nucleic        acid of said library being capable of being packaged using said        component of an rgdp;    -   expressing in a recombinant host organism said first polypeptide        chain component part fused to a component of a rgdp or        population thereof and said second polypeptide chain component        part of an sbp member or a population thereof, to produce a        library of rgdps each displaying at its surface an sbp member        and containing nucleic acid encoding a first and a second        polypeptide chain component part of the sbp member displayed at        its surface.

Readers are urged to consult WO92/01047, in particular, if furtherdetails of any method described herein are desired.

In one embodiment of the present invention both first and secondpolypeptide chain component parts or populations thereof are expressedfrom nucleic acid capable of being packaged using said component of anrgdp. This might ire when the component parts together form a Fabfragment or, more usually, when each said sbp member displayed at thesurface of an rgdp is an scFv antibody fragment.

In one embodiment, each said second polypeptide chain component part orpopulation thereof may be expressed from nucleic acid separate fromnucleic acid from which said first polypeptide chain component part orpopulation thereof is expressed. The nucleic acid encoding the firstpolypeptide chain component part may be on the same expression vector asthe nucleic acid encoding the second polypeptide chain component part,but separate from it so that, for example, Fab fragments are produced.Alternatively, the nucleic acid encoding the first polypeptide chaincomponent part may be on a different expression vector from the nucleicacid which encodes a second polypeptide chain component part. Where afirst and second polypeptide chain component part are both encoded onthe same expression vector then they may be expressed as scFv fragments,where a VH domain is joined to a VL domain by a polypeptide linker, sothat each scFv is a single polypeptide chain.

Each sbp member displayed at the surface of an rgdp is an Fab antibodyfragment.

The nucleic aced may be derived from, e.g. rearranged V genes of, anunimmunised mammal, for example a mouse, rat, rabbit, sheep, pig, horse,goat, dog or human. Preferably the species of mammal is human, since itis most difficult to obtain antibodies which recognise (i.e. bindspecifically) human self antigens.

The nucleic acid may be derived from a library prepared by artificial orsynthetic recombination of V-gene segments, which may be germ-lineV-gene sequences. The library may be totally synthetic.

Sbp members selected in (b) displayed at the surface of rgdps may beselected or screened to provide an individual sbp member or a mixedpopulation of said sbp members associated in their respective rgdps withnucleic acid encoding said sbp member or a polypeptide chain thereof.Rgdp phase displaying sbp members selected in (b) may be grown toincrease their numbers before any subsequent further selection orscreening. Nucleic acid which encodes a selected or screened sbp memberand which is derived from an rgdp which displays at its surface aselected or screened sbp member may be used to express an sbp member ora fragment of derivative thereof in a recombinant host organism.

The present invention encompasses any method wherein nucleic acid fromone or more rgdps selected from the library by binding with a selfantigen is taken and used to provide encoding nucleic acid in a furthermethod (according to any embodiment of the present invention or not) toobtain an individual sbp member or a mixed population of sbp members, orencoding nucleic acid therefor.

The expression end product, selected sbp member, may be modified toproduce a derivative thereof.

The expression end product or derivative thereof may be used to preparea therapeutic or prophylactic medicament or a diagnostic product.

The present invention also encompasses antibody fragments, derivativesthereof, including whole antibodies and fusions with enzymes, obtainedusing any method described herein according to the present invention.

According to an aspect of the present invention there is provided use,in any method according to embodiment of the present invention describedhe a kit comprising a library of vectors each comr nucleic acid which iscapable of being packag and which encodes a polypeptide chain componentpart of an antibody for display at the surface of rgdps.

There is also provided by the present invention use, in any methodaccording to any embodiment of the present invention described herein,of a kit comprising a library of rgdps each containing nucleic acidencoding at least one polypeptide chain component part of an antibody.

The present invention provides generally a method for producing areplicable genetic display package (rgdps) or population of such rgdps,which method comprises the steps of:

(a) inserting a nucleotide sequence encoding a binding molecule which isa member of a specific binding pair and an anti-self antibody, within aviral genome;

(b) culturing the virus containing said nucleotide sequence so that saidbinding molecule is expressed and displayed by the virus at its surface.

The present invention also provides a method for selecting a rgdpspecific for a particular self-antigen epitope which comprises producinga population of such rgdps and the additional step of selecting for saidbinding molecule which is an anti-self antibody by contacting thepopulation with said epitope so that individual rgdps with the desiredspecificity may bind to said epitope. The method may comprise one ormore of the additional steps of: (i) separating any bound rgdps from theepitope; (ii) recovering any separated rgdps and (iii) using theinserted nucleotide sequences from any separated rgdps in a recombinantsystem to produce the binding molecule separate from the virus. Theselection step may isolate the nucleotide sequence encoding the bindingmolecule of desired specificity, by virtue of said binding moleculebeing expressed in association with the surface of the virus in whichsaid encoding nucleic acid is contained.

The present invention also provides a method of producing a multimericmember of a specific binding pair (sbp) which is an anti-self antibody,which method comprises:

-   expressing in a recombinant host organism a first polypeptide chain    of said sbp member or a genetically diverse population of said sbp    member fused to a component of a secreted replicable genetic display    package (rgdp) which thereby displays said polypeptide at the    surface of the package, and expressing in a recombinant host    organism a second polypeptide chain of said multimer and causing or    allowing the polypeptide chains come together to form said multimer    as part of said rgdp at least one of said polypeptide chains being    expressed from nucleic acid that is capable of being packaged using    said component therefor, whereby the genetic material Of each said    rgdp encodes a said polypeptide chain.

Both said chains may be expressed in the same host organism.

The first and second chains of said multimer may be expressed asseparate chains from a single vector containing their respective nucleicacid.

At least one of said polypeptide chains (or polypeptide chain componentparts) may be expressed from a phage vector.

At least one of said polypeptide chains may be expressed from a phagemidvector, the method including using a helper phage, or a plasmidexpressing complementing phage genes, to help package said phagemidgenome, and said component of the rgdp is a capsid protein therefor. Thecapsid protein may be absent, defective or conditionally defective inthe helper phage.

The method may comprise introducing a vector capable of expressing saidfirst polypeptide chain, into a host organism which expresses saidsecond polypeptide chain in free form, or introducing a vector capableof expressing said second polypeptide in free form into a host organismwhich expresses said first polypeptide chain.

Each of the polypeptide chain may be expressed from nucleic acid whichis capable of being packaged as a rgdp using said component fusionproduct, whereby encoding nucleic acid for both said polypeptide chainsare packaged in respective rgdps.

The fusions may be expressed in the absence of the rgdp displaycomponent, perhaps capsid, expressed in wild-type form.

The capsid protein may be absent, defective or conditionally defectivein the helper phage.

The host cell may be a mutator strain which introduces genetic diversityinto the sbp member nucleic acid.

The rgdp may be a bacteriophage, the host a bacterium, and saidcomponent of the rgdp a capsid protein for the bacterophage. The phagemay be a filamentous phage. The phage may be selected from the class Iphages fd, M13, f1, If1, lke, ZJ/Z, Ff and the class II phases Xf, Pf1and Pf3. The phage may be fd or a derivative of fd. The derivative maybe tetracycline resistant. The said sbp member or polypeptide chainthereof man be expressed as a fusion with the gene III capsid protein ofphage fd or its counterpart in another filamentous phage. The sbp memberor polypeptide chain thereof may be inserted in the N-terminal region ofthe mature capsid protein downstream of a secretory leader peptide. Thesequence may be inserted after amino acid+1 of the mature protein. Thesite for insertion may be flanked by short sequences corresponding tosequences which occur at each end of the nucleic acid to be inserted.

The host may be E. coli.

Nucleic abed encoding an sbp member polypeptide may be linked downstreamto a viral capsid protein through a suppressible translational stopcodon, so that under conditions where the stop is supressed fusionproteins are produced comprising sbp member polypeptide and viral capsidprotein, while under non-supressing conditions free form sbp memberpolypeptides are produced.

Selection systems and assay formats are discussed elsewhere in thistext. In these systems and formats, the gene sequence encoding thebinding molecule (eg. the antibody) of desired specificity is separatedfrom a general population of rgdps having a range of specifies, by thefact of its binding to a specific target (eg the antigen or epitope).Thus the rgdps formed by said expression may be selected or screened toprovide an individual sbp member or a selected mixed population of saidsbp members associated in their respective rgdps with nucleic acidencoding said sbp member or a polypeptide chain thereof. The rgdps maybe selected by affinity with a member complementary to said sbp member.

Any rgdps bound to said second member may be recovered by washing withan eluant. The washing conditions may be varied in order to obtain rgdpswith different binding affinities for said epitope. Alternatively, toobtain eg high affinity rgdps, the complementary member (eg an epitope)may be presented to the population of rgdps (eg pAbs) already bound to abinding member in which case pAbs with a higher affinity for the epitopewill displace the already bound binding member. Thus the eluant maycontain a molecule which competes with said rgdp for binding to thecomplementary sbp member. The rgdp may be applied to said complementarysbp member in the presence of a molecule which competes with saidpackage for binding to said complementary sbp member. Nucleic acidderived from a selected or screened rgdp may be used to express said sbpmember or a fragment or derivative thereof in a recombinant hostorganism. Nucleic acid from one or more rgdps may be taken and used toprovide encoding nucleic acid in a further said method to obtain anindividual sbp member or a mixed population of sbp members, or encodingnucleic acid therefor. The expression end product may be modified toproduce a derivative thereof.

A preferred source for the generation of diverse libraries fromunimmunised humans is IgM mRNA. It is was found in example 43 ofWO92/01047 that antibody fragments directed against turkey egg lysozymeand 2-phenyl-5-oxazolone were much more readily isolated from a phagelibrary derived from the IgM mRNA from unimmunised human donors, thanfrom one prepared from IgG mRNA. Furthermore, no 2-phenyl-5-oxazolonebinding antibody fragments could be isolated from a library of 2000000phage antibody clones prepared from IgGmRNA of unimmunised mice (T.Clackson et al, Nature 352 624-628.1991). Examples 1 to 3 of thisapplication show the isolation of antibodies specific for self antigenfrom the IgM library. Although in these samples, antiself specificitieshave been selected as single chain Fv fragments in a single repliconformat, antibody specificities could be selected as Fab fragments in asingle replicon format or in a dual combinatorial, dual replicon formatHoogenboom et al, 1991 supra) for instance using recombination with theloxP system (PCT/GB92/00883).

Phage libraries may be prepared which are enriched for antibodiesdirected against self. B lymphocytes express surface IgM and surface IgDbefore stimulation with antigen but express little soluble IgM or IgD.These unstimulated cells are more likely to contain antibody genes withanti-self specificities. In contrast, terminally differentiated plasmacells which secrete soluble antibodies express little surfaceimmunoglobulin. The preparation of cDNA for phage library preparationusing primers which are specific for surface IgM or surface IgD willproduce a repertoire of antibody genes enriched for the naive,unselected genes encoding V domains. In B lymphocytes which have beenfunctionally silenced by exposure to self there are greatly reducedlevels of surface IgM but unchanged levels of surface IgD (C. C. Goodnowet al. supra). Hence, a primer specific for surface IgD may beparticularly suitable for isolation of anti-self antibodies.

However, as demonstrated in this application, IgM mRNA from unselectedperipheral blood lymphocytes is one preferred source of V genes forantiself specificities. Other sources of such anti-self antibodies maybe fetal mRNA or cord blood mRNA (P. M. Lydyard et al Scand J Immunol 3133-43, 1990).

There is the potential for making repertoires for phage display usingthe original combination of VH and VL domains by the use of PCR andlinkage of the genes encoding them within cells expressing thesedomains. The principle of ‘In cell PCR’, where the original VH/VLpairing is maintained, was demonstrated in PCT/GB92/01483 and describedin Embleton et al in Nucleic Acids Res., 20, 3831-3837, 1992. This maybe particularly useful if lymphocytes can be selected at a stage beforethe deletion of clones expressing anti-self antibodies.

In one embodiment of this invention, V gene sequences, or even librariesprepared by the synthetic recombination of V, D and J segments may beused. These act as a rich source of anti-self antibodies. In examples 5to 7, we demonstrate that anti-self specificities against TNF, humananti-rhesus D antibody (OAK3) and human thyroglobulin can be isolatedfrom a phage antibody library prepared by the synthetic joining of V. Dand J segments. The use of germ line V genes for this purpose, as shownin examples 5 to 7, should be valuable for the isolation of anti-selfantibodies as there is some evidence that B lymphocytes directed againstsoluble self antigens are functionally silenced A; and those directedagainst multivalent membrane bound self antigen are eliminated (S. B.Hartley et al supra; D. M. Russell et al, supra). Thus, the use ofsynthetic libraries made by VH, DH, JH or VK,JK or VL,JL recombinationin vitro or its equivalent may be particularly advantageous forisolation of antibodies directed against multivalent membrane bound selfantigens.

In examples 5 to 7 we have used synthetic VH CDR3 segments incorporatingsequences of random bases at the V-D-J joining region and linked them togerm line VH gene segments. Other strategies may be used such as makingeach of the CDR loops of random sequence or making the CDR loops ofknown canonical structures (C. Chothia et al, Nature 342 877-893, 1989)and incorporating random sequence elements. The germ line nature of theV and J segments could be altered by incorporation of specific or randomalterations to the sequence or by using somatically mutated V generegions. The strategy used in examples 5 to 7 has the advantage that theloop structures of the V gene segments form only a limited number ofdistinct folds and combinations of folds (C. Chothia et al J. Mol. Biol.227 779-817, 1992) and have presumably evolved for stability and tocreate a distribution and range of binding sites well suited to matchthe structure of antigens. Moreover, the framework regions and first twohypervariable loops of both heavy and light chains of the synthetichuman antibodies are likely to be identical in many differentindividuals. Such synthetic human antibodies could be less immunogenicthan entirely artificial structures.

A further but less preferred alternative to the above natural andsynthetic phage display libraries would be to prepare random mutagenesislibraries displayed on phage, derived from one or a few human antibodymolecules and selecting anti-self antigen specificities from these.

Selection

Individual rgdps eg pAbs expressing the desired specificity for anantigen, can be isolated from a library using the conventional screeningtechniques (e.g. as described in Harlow, E., and Lane, D., 1988, supraGherardi, E et al. 1990. J. Immunol. meth. 126 p 61-68).

The applicants have also devised selection techniques that arepracticable because of the unique properties of rgdps. The generaloutline of some screening procedures is illustrated in FIG. 5 using pAbsas an example type of rgdp.

The population/library of pAbs to be screened could be generated fromimmunised or other animals; or be created in vitro by mutagenisingpre-existing phage antibodies (using techniques well-known in the artsuch as oligonucleotide directed mutagenesis (Sambrook, J., et al., 1989Molecular Cloning a Laboratory Manual, Cold Spring Harbor LaboratoryPress) but are preferably derived from unimmunised humans or artificialrecombination of human V segments, as described elsewhere. Thispopulation can be screened in one or more of the formats described belowwith reference to FIG. 5, to derive those individual pAbs whose antigenbinding properties are different from sample c.

Binding Elution

FIG. 5(i) shows antigen (ag) bound to a solid surface (s) the solidsurface (s) may be provided by a petri dish, chromatography beads,magnetic beads and the like. The population/library of pAbs is thenpassed over the ag, and those individuals p that bind are retained afterwashing, and optionally detected with detection system d. A detectionsystem based upon anti-fd antisera may be used (see, for instance,Example 4 of WO92/01047). If samples of bound population p are removedunder increasingly stringent conditions, the binding affinityrepresented in each sample will increase. Conditions of increasedstringency can be obtained, for example, by increasing the time ofsoaking or changing the pH of the soak solution, etc.

Competition

Referring to FIG. 5(ii) antigen ag can be bound to a solid support s andbound to saturation by the original binding molecule c. If a populationof mutant pAb (or a set of unrelated pAbs) is offered to the complex,only those that have higher affinity for antigen ag than c will bind. Inmost examples, only a minority of population c will be displaced byindividuals from population p. If c is a traditional antibody molecule,all bound material can be recovered and bound p recovered by infectingsuitable bacteria and/or by use of standard techniques such as PCR.

An advantageous application is where ag is used as a receptor and c thecorresponding ligand. The recovered bound population p is then relatedstructurally to the receptor binding site/and or ligand. This type ofspecificity is known to be very useful in the pharmaceutical industry.

Another advantageous application is where ag is a antibody and c itsantigen. The recovered bound population p is then an anti-idiotypeantibody which have numerous uses an research and the diagnostic andpharmaceutical industries.

At present it is difficult to select directly for anti-idiotypeantibodies. pAbs would give the ability to do this directly by bindingpAb libraries (eg a naive library) to B cells which express antibodieson their surface) and isolating those phage that bound well.

In some instances it may prove advantageous to pre-select population p.For example, in the anti-idiotype example above, p can be absorbedagainst a related antibody that does snot end the antigen.

However, If c is a pAb, then either or both c and p can advantageouslybe marked in some way to both distinguish and select for bound p overbound c. This marking can be physical, for example, by pre-labelling pwith biotin; or more advantageously, genetic. For example, c can bemarked with an EcoB restriction site, whilst p can be marked with anEcoK restriction site (see Carter, P. et al., 1985, Nucl. Acids Res. 13,4431-4443). When bound p+c are eluted from the antigen and used toinfect suitable bacteria, there is restriction (and thus no growth) topopulation c (i.e. EcoB restricting bacteria in this example). Any phagethat grew, would be greatly enriched for those individuals from p withhigher binding affinities. Alternatively, the genetic marking can beachieved by marking p with new sequences, which can be used tospecifically amplify p from the mixture using PCR.

Since the bound pAbs can be amplified using for example PCR or bacterialinfection, it is also possible to rescue the desired specificity evenwhen insufficient individuals are bound to allow detection viaconventional techniques.

The preferred method for selection of a phage displaying a proteinmolecule with a desired specificity or affinity will often be elutionfrom an affinity matrix with a ligand. Thus, self antigen or fragmentsthereof may be used to elute specific phage antibodies from self antigenbound to a matrix. Alternatively, the homologous antigen from adifferent species may be bound to a matrix, a phage antibody librarybound, and phage antibodies specific for the self antigen may be elutedusing self antigen. For instance, a bovine antigen may be bound to thematrix, a human phage antibody library bound and human antigen used forelution. Antiself antibodies thus isolated will be specific for epitopesshared between the bovine and human antigens. A further but lesspreferred alternative may be to bind the phage non-specifically to acolumn and elute with self antigen. For instance, if a Fab phage libraryis bound to an anti-Fab affinity column, it may be washed at a pH whichdoes not elute non-specific phage and then washed with solution which isthe same except it contains self antigen, eluting by virtue of thehigher affinity for the mobile phase of phage expressing antibodiesagainst the self antigen.

For each of these formats elution with increasing concentrations ofligand should elute phage displaying binding molecules of increasingaffinity. However, when eg a pAb binds to its antigen with high affinityor avidity (or another protein to its binding partner) it may not bepossible to elute the pAb from an affinity matrix with molecule relatedto the antigen.

Alternatively, there may be no suitable specific eluting molecule thatcan be prepared in sufficiently high concentration. In these cases it isnecessary to use an elution method which is not specific to eg theantigen-antibody complex. Some of the non-specific elution methodsgenerally used reduce phage viability for instance, phage viability isreduced with time at pH12 (Rossomando, E. F. and Zinder N. D. J. Mol.Biol. 36 387-399 1968). There may be interactions between eg antibodiesand affinity matrices which cannot be disrupted without completelyremoving phage infectivity. In these cases a method is required to elutephage which does not rely on disruption of eg the antibody—antigeninteraction. A method was therefore devised which allows elution ofbound pAbs under mild conditions (reduction of a dithiol group withdithiothreitol) which do not disrupt phage structure (Example 47 ofWO92/01047).

The method of mild elution uses binding of the phage antibody populationto biotinylated antigen and binding to streptavidin magnetic beads.Following washing to remove non-binding phage, the phage antibody iseluted and used to infect cells to give a selected phage antibodypopulation. A disulphide bond between the biotin and the antigenmolecule allows mild elution with dithiothreitol. A particularlyadvantageous way of performing this selection is to use biotinylatedantigen in excess but at or below a concentration equivalent to thedesired dissociation constant for the antigen-antibody binding. Thismethod is advantageous for the selection of high affinity antibodies (R.E. Hawkins, S. J. Russell and G. Winter J. Mol. Biol. 226 889-896,1992). Antibodies may also be selected for slower off rates for antigenselection as described in (R. E. Hawkins et al, 1992 supra). Theconcentration of biotinylated antigen may gradually be reduced to selecthigher affinity phage antibodies. As an alternative, the phage antibodymay be in excess over biotinylated antigen in order that phageantibodies compete for binding, in an analagous way to the competitionof peptide phage to biotinylated antibody described by J. K. Scott & G.P. Smith (Science 249 386-390, 1990).

This elution procedure is just one example of an elution procedure undermild conditions. A particularly advantageous method would be tointroduce a nucleotide sequence encoding amino acids constituting arecognition site for cleavage by a highly specific protease between theforeign gene inserted, in this instance a gene for an antibody fragment,and the sequence of the remainder of gene III. Examples of such highlyspecific proteases are Factor X and thrombin. After binding of the phageto an affinity matrix and elution to remove non-specific binding phageand weak binding phage, the strongly bound phage would be removed bywashing the column with protease under conditions suitable for digestionat the cleavage site. This would cleave the antibody fragment from thephage particle eluting the phage. These phage would be expected to beinfective, since the only protease site should be the one specificallyintroduced. Strongly binding phage could then be recovered by infectingeg. E. coli TG1 cells.

An alternative procedure to the above is to take the affinity matrixwhich has retained the strongly bound pAb and extract the DNA, forexample by boiling in SDS solution. Extracted DNA can then be used todirectly transform E. coli host cells or alternatively the antibodyencoding sequences can be amplified, for example using PCR with suitableprimers such as those disclosed herein, and then inserted into a vectorfor expression as a soluble antibody for further study or a pAb forfurther rounds of selection.

Another preferred method for selection according to affinity would be bybinding to an affinity matrix containing low amounts of ligand.

If one wishes to select from a population of phages displaying a proteinmolecule with a high affinity for its ligand, a preferred strategy is tobind a population of phage to an affinity matrix which contains a lowamount of ligand. There is competition between phage, displaying highaffinity and low affinity proteins, for binding to the ligand on thematrix. Phage displaying high affinity protein is preferentially boundand low affinity protein is washed away. The high affinity protein isthen recovered by elution with the ligand or by other procedures whichelute the phage from the affinity matrix (Example 35 of WO92/01047demonstrates this procedure).

In summary then, for recovery of the packaged DNA from the affinitystep, the package can be simply eluted, it can be eluted in the presenceof a homologous sbp member which competes with said package for bindingto a complementary sbp member; it could be removed by boiling, it couldbe removed by proteolytic cleavage of the protein; and other methodswill be apparent to those skilled in the art eg. destroying the linkbetween the substrate and complementary sbp member to release saidpackaged DNA and sbp member. At any rate, the objective is to obtain theDNA from the package so that it can be used directly or indirectly, toexpress the sbp member encoded thereby.

The efficiency of this selection procedure for pAbs and the ability tocreate very large libraries means that the immunisation techniquesdeveloped to increase the proportion of screened cells producingantibodies of interest will not be an absolute requirement. Thetechnique allows the rapid isolation of binding specificities egantigen-binding specificities, including those that would be difficultor even unobtainable by conventional techniques, for example, catalyticor anti-idiotypic antibodies. Removal of the animal altogether is nowpossible, once a complete library of the immune repertoire has beenconstructed.

Applications of Antibodies to Self Antigens

Human antibodies to cell surface components The isolation of suchantibody specificities would be particularly useful for preparing agentswhich mediate cell killing for instance of cancer cells, for exampleusing the natural effector function of antibodies. Anti-self antibodiesmay also be valuable in the preparation of diagnostic in vivo imagingreagents, for instance using radioisotopes.

Antibodies directed against cell surface components of specific T-cellsubsets could be used therapeutically (D. Wraith et al Cell 57709-715,1989; L. Steinman and R. Mantegazza FASEB J. 4 2726-2731,1990),for instance to prevent T cell action causing rheumatoid arthritis.

Human Antibodies Modifying the Function of Self Molecules

Antibodies can be isolated which modify the action of self moleculessuch as hormones, growth factors and receptors through their binding toa specific epitope on the molecule. Multifunctional proteins may haveboth desirable and undesirable characteristics, particularly if they areused therapeutically. For instance, the lymphokine TNF (tumour necrosisfactor) binds to, at least two different classes of cell receptors—onecommonly found on vascular endothelial cells, the other commonly foundon tumour cells. A mouse antibody to TNF has been made which preventsTNF from binding to endothelial cell receptors while still allowing itto bind to tumour cells thus allowing attack on the tumours withouttoxic side effects mediated through endothelial cells (Patentapplication PCT/AU90/00337). For therapeutic use of antibody modifiersof hormone or growth factor molecules, it would be preferable to have ahuman antibody specificity isolated directly through selection from aphage library.

Human Anti-Idiotypes

Anti-idiotype antibodies (antibodies directed against the antigencombining sites formed by the variable domains of human antibodies) areconventionally made by isolating an antibody against an antigen and thenusing this isolated antibody as an immunogen to raise antibodiesdirected against it. If the original antibody is directed against ahormone or growth factor, the relationship between antigen and antibodycombining sites means that the anti-idiotype may mimic in some aspectsthe hormone or growth factor and bind to the receptor for thesemolecules. However, the fraction of anti-idiotype antibodies able tomimic the binding of the hormone to the receptor would be expected to besmall. Furthermore, the deletion of antiself lymphocytes would mean thatusing the conventional route to antiidiotypes would be difficult for theisolation of human anti-idiotype antibodies mimicking molecules bindinghuman receptors. In this application we show that antibodies directedagainst the antigen combining sites formed by the variable domains ofhuman antibodies may be directly isolated from phage antibody displaylibraries, as shown in examples 1 and 4, and it should also be possibleto identify the anti-idiotypic antibodies mimicking the binding of thehormone directly by screening for binding to the receptor.

Anti-idiotypes may also be useful for the treatment of autoimmunedisease. They could be used to bind to circulating autoantibodies.However, it may be preferable to attack directly antibody producingcells, for instance using a bispecific antibody directed against a cellsurface marker as well as an anti-idiotype specificity. Alternatively,plasmaphoresis could be used to remove circulating antibody and thecells treated directly.

Human Antibodies Against Receptors

Human antibodies that bind to receptors, blocking or antagonising ligandfunction could be selected directly from a phage library displayingantibodies derived from an unimmunised donor.

Human Antibodies to Prevent Transplant Rejection

Antibodies directed against the major histocompatibility complexproteins could be used to treat patients following transplants, ororgans prior to transplantation, in order to prevent rejection.Antibodies directed against several lymphocyte cell surface markers havebeen used for the prevention of rejection in transplants e.g. CD45, CD3,CD4, CD8 and interleukin-2 receptor. Example 3 shows that humanantibodies against CD4 can be directly isolated from phage displaylibraries.

Human Antibodies Against Cytokines

Human antibodies against cytokines would be valuable for treatment ofhuman disease, for example of septic shock with anti-TNF andanti-interleukin 1 antibodies. Examples 1 and 6 show that humanantibodies against TNF can be isolated directly from phage antibodylibraries derived from unimmunised humans or the synthetic recombinationof V,D and J fragments. In many cases these cytokine molecules arestrongly conserved between species, for instance transforming growthfactory-β (TGF-β), and it has proved difficult to isolate antibodiesdirected against the human molecule even in mice. The isolation of humananti-self antibodies as described in this invention provides a method ofobtaining human antibodies with such a specificity.

Human Antibodies for diagnosis and treatment of Cardiac Disorders

Human antibodies against clot components e.g. fibrin, would be usefulfor imaging clots when labelled with radioactivity or for dissolvingclots, if for example linked to a clot dissolving enzyme such asurokinase.

Antibodies triggering Receptor Function

Antibodies may be selected that bind to a cell receptor and trigger abiological response in the cell. This is described n more detail belowand in Example 8 describes the isolation of such antibodies.

By cycles of growth and selection, those rgdps binding to the cellreceptors are isolated. Some of these rgdps encode binding specificitieswith the potential (alone or in combination with other bindingspecificities) to trigger the receptors. These binding specificities aretested alone, or in combination, for triggering the cell receptors.

There are a variety of cell receptors in which the binding of a ligand,for example hormone, growth factor, or peptide triggers a biologicalevent, for example the activation of tyrosine kinase activity, or theopening of an ion channel. The rdgps could be selected for binding tocell receptor (or a related receptor with conserved portions of surfacesuch as from another species), for example by using cells displaying thecell receptor, or using soluble receptor immobilised on solid phase, orusing domains or peptide epitopes of the receptor. Ideally the receptorwould be provided in a crosslinked form (as required for itstriggering).

Triggering of receptors at the cell surface often seems to involve therelative movement of proteins or subunits. For example, in theneurotransmitter-gated receptors, the five subunits that are arrangedsymmetrically An the membrane place, delineate an ion pathway down thecentre. Binding of the neurotransmitter is thought to alter the size ofthe central ion channel by causing small rearrangements between thesubunits in an allosteric transition. For tyrosine kinase receptors, theligand appears to drive receptor oligomerisation. Thus antibodies withbinding specificities directed against a receptor may have the potentialto promote an allosteric change or to promote oligomerisation. Theoligomerisation of the receptors may also be promoted by using bivalentor bispecific antibodies.

The soluble antibodies or antibody fragments may be monovalentfragments, for example, single chain Fv fragments or Fab fragments, orbivalent fragments, for example, Fab₂ or complete antibody fragments.The bivalency could also be promoted in other ways, for example (1) byencoding a tag, such as a peptide or protein (for example, the subunitof a dimeric protein) that self associates, at the N or C-terminus ofthe monomeric fragment, (2) using a bivalent antibody that binds to themonovalent fragment, for example, to a common C-terminal tag, or to anantibody constant domain (3) chemical cross-linking.

Bispecific antibody or bispecific fragments could also be made as forthe bivalent fragments. (For expression of the bispecific antibody orfragment in the same cell, the genes encoding both specificities wouldneed to be introduced together). The different antibody “arms” could bedirected against the same receptor, for example to different epitopes,or to two different receptors (to trigger hybrid receptors).

The direct isolation of anti-self antibodies from phage libraries asdescribed in this invention is important to allow a large number ofantibodies to be surveyed for these triggering receptors.

It is appropriate to distinguish the making of antibodies to triggerreceptors as is described here and provided as an aspect of the presentinvention from the “anti-idiotypic route” in which specific antibodiesraised in an animal, including man, by vaccinating the said animal witha specific antigen are themselves used to vaccinate another animal, newantibodies termed anti-idiotypic antibodies (Anti-Ids) being producedable to recognise and bind to the first set of antibodies. Some speciesof these Anti-Ids are able to mimic the specific biological propertiesof the original antigen. If for example, the antigen were a peptidehormone or a cell receptor, the Anti-Id to the hormone or cell receptorantigen is able to elicit a response of the cell (See Gaulton, G. N. andGreane, M. I., 1986. Idiotypic mimicry of biological receptors. Ann.Rev. Immunol. 4,253-280: Sege, K. and Peterson, P. A., 1978. Use ofanti-idiotypic antibodies as cell surface receptor probes. Proc. Natl.Acad. Sci. Usa. 75, 2443-2447 for examples).

The essence of current teaching of Anti-Ids as mimics of antigens isthat they are produced as a result of constructing antibodies toantibodies of the original antigen. There is however, some controversyover whether such anti-idiotypes accurately mimic the original antigen(S. J. Davis et al Nature 358 76-79, 1992).

There is therefore a clear distinction between antibodies prepared by ananti-idiotypic route that mimic antigens such as growth factors orhormones, and antibodies that are made directly to the receptors totrigger the receptors. The antibodies derived by an anti-idiotypic routerequire the antigen (hormone, growth factor) and will bind to the sameepitope on the receptor as the hormone, while the antibodies derived bybinding to the receptors need not bind to the same epitope to triggerthe receptor. Indeed such antibodies need not mimic a known hormone orgrowth factor, as their specificity, or binding to receptor(characterised as epitope, on-rate or off-rate) or blood clearance islikely to differ. The process for making the antibodies is also quitedifferent. Anti-idiotypic antibodies are made classically byimmunisation of animals, although they can be isolated directly fromphage display libraries as described above. Antibodies directed againstself receptors are made by selection from V-gene libraries (as describedabove).

As well as the advantages over the anti-idiotypic route, the antibodiesderived directly by receptor binding may even have advantages over thenatural hormone or growth factor. Thus receptors that are defective forbinding of the natural hormone or growth factor (for example in agenetic disease), may be triggered by an antibody binding at a differentepitope.

As therapeutic agents the various isotypes of antibodies or fragments ofantibodies carrying the variable regions responsible for the specificityof the molecule have a number of properties having advantages over thebioactive moiety they mimic. For example, unlike the natural hormonestheir half-life in circulation can be modified readily. Depending on theantibody isotype or fragment chosen, they have half-lives in circulationin a patient ranging from minutes to several weeks. If long term usageor short term clearance is required this can easily be accommodated bychoosing the appropriate antibody isotype without need to use slowrelease devices as implants, or continuous intravenous infusion, etc.

Furthermore, many hormones or tissue growth factors or antigens ingeneral are functionally complex with different epitopes of each of themolecules having various specific functions. Clones of antibody mimicsare monofunctional in this respect so could be used to produce onespecific biological effect of a hormone without a second effect whichlatter effect may be disadvantageous to the patient. Thus the lymphokineTNF (tumour necrosis factor) binds to two different classes of cellreceptors—one common on vascular endothelial cells, the other common ontumour cells. If the TNF is modified so that it cannot bind to theendothelial cell receptors but can still bind to tumour cell receptors,the tumours are attacked without at the same time inducing the verytoxic side effects mediated through the vascular receptors. (This isdescribed in Australian Patent Application PCT/AU90/00337). An antibodymimic able to recognise the tumour cell receptor would be expected to bevery specific and kill tumour cells without inducing toxic side effectsmediated through the vascular endothelium since it would have noresemblance to the TNF epitope which binds to receptors on the latter.

Terminology

Much of the terminology discussed in this section has been mentioned inthe text where appropriate.

Self

A self antigen is an antigen or epitope which is capable of binding toan antigen binding site formed by antibody variable domain(s) and whichis conserved between members of a species of animal and native to thebody.

The immune system tries to avoid making antibodies to self antigens. Ithas been suggested that (i) sequences of germ line V gene segments havebeen evolved under pressure to be directed towards foreign, e.g.pathogen, antigens and epitopes, and away from being able to provideantibodies which will bind self antigens, and (ii) that, in addition tothis, immune tolerance causes those combinations of gene segmentsencoding anti-self antibody which do arise, to be deleted or anergised.Consequently, there are not normally circulating antibodies againstthese antigens except in disease states, eg autoimmune diseases. A selfantigen may be one which does not vary between individuals of a species.A self antigen may be one for which there is normal allelic variationthroughout a population. Immunisation of one individual in a specieswith a self antigen would not normally be expected to result ingeneration, or detection, of antibodies to the antigen, except perhapswhen tolerance is deliberately broken. Antibodies to a self-antigen mayonly be present in an individual who is suffering from autoimmunedisease. On the other hand, there are some self antigens to whichcirculating antibodies can be found in a sub-population of normalindividuals of a species.

A self antigen may be an antigen recognised by B-cell surface antibodiesbut not by antibodies which can be found circulating. It might not bepossible to detect or obtain circulating antibodies to a self antigenexcept perhaps when the individual is suffering from an autoimmunedisease or syndrome.

An anti-self antibody or antibody fragment is an antibody or fragmentthereof which has binding specificity for a self antigen. It mayrecognise an epitope which is found only on a self antigen, or it may becross-reactive with an antigen which individuals of the species willrecognise as foreign. The present invention is particularly well suitedto the production and isolation of antibody fragments which bind only aself antigen.

Specific Binding Pair

This describes a pair of molecules (each being a member of a specificbinding pair) which are naturally derived or synthetically produced. Oneof the pair of molecules, has an area on its surface, or a cavity whichspecifically binds to, and is therefore defined as complementary with aparticular spatial and polar organisation of the other molecule, so thatthe pair have the property of binding specifically to each other.Examples of types of specific binding pairs are antigen-antibody,biotin-avidin, hormone-hormone receptor, receptor-ligand,enzyme-substrate, lgG-protein A.

Multimeric Member

This describes a first polypeptide which will associate with at least asecond polypeptide, when the polypeptides are expressed in free formand/or expressed on the surface of a substrate. The substrate may beprovided by a bacteriophage. Where there are two associatedpolypeptides, the associated polypeptide complex is a dimer, where thereare three, a trimer etc. The dimer, trimer, multimer etc or themultimeric member may comprise a member of a specific binding pair.

Example multimeric members are heavy domains based on an immunoglobulinmolecule, light domains based on an immunoglobulin molecule, T-cellreceptor subunits.

Replicable Genetic Display Package (Rgdp)

This describes a biological particle which has genetic informationproviding the particle with the ability to replicate. The particle candisplay on its surface at least part of a polypeptide. The polypeptidecan be encoded by genetic information native to the particle and/orartificially placed into the particle or an ancestor of it. Thedisplayed polypeptide may be any member of a specific binding pair eg.heavy or light chain domains based on an immunoglobulin molecule, anenzyme or a receptor etc.

The particle may be a virus eg. a bacteriophage such as fd or M13.

Package

This describes a replicable genetic display package in which theparticle is displaying a member of a specific binding pair at itssurface. The package may be a bacteriophage which displays an antigenbinding domain at its surface. This type of package has been called aphage antibody (pAb).

Antibody

This describes an immunoglobulin whether natural or partly or whollysynthetically produced. The term also covers any protein having abinding domain which is, or is homologous to, an immunoglobulin bindingdomain. These proteins can be derived from natural sources, or partly orwholly synthetically produced.

Example antibodies are the immunoglobulin isotypes and the Fab, F(ab¹)₂,scFv, Fv, dAb, Fd fragments.

Immunoglobulin Superfamily

This describes a family of polypeptides, the members of which have atleast one domain with a structure related to that of the variable orconstant domain of immunoglobulin molecules. The domain contains twoβ-sheets and usually a conserved disulphide bond (see A. F. Williams andA. N. Barclay 1988 Ann. Rev Immunol. 6, 381-405).

Example members of an immunoglobulin superfamily are CD4, plateletderived growth factor receptor (PDGFR), intercellular adhesion molecule.(ICAM). Except where the context otherwise dictates, reference toimmunoglobulins and immunoglobulin homologs in this application includesmembers of the immunoglobulin superfamily and homologs thereof.

Homologs

This term indicates polypeptides having the same or conserved residuesat a corresponding position in their primary, secondary or tertiarystructure. The term also extends to two or more nucleotide sequencesencoding the homologous polypeptides.

Example homologous peptides are the immunoglobulin isotypes and the TIMbarrel enzymes.

Functional

In relation to a sbp member displayed on the surface of a rgdp, meansthat the sbp member is presented in a folded form in which its specificbinding domain for its complementary sbp member is the same or closelyanalogous to its native configuration, whereby it exhibits similarspecificity with respect to the complementary sbp member.

Genetically Diverse Population

In connection with sbp members or polypeptide components thereof, thisis referring not only to diversity that can exist in the naturalpopulation of cells or organisms, but also diversity that can be createdby artificial mutation in vitro or in vivo.

Mutation in vitro may for example, involve random mutagenesis usingoligonucleotides having random of nucleotide sequences downstream of thecodon under one set of conditions, but under another set of conditionstranslation ends at the codon. Example of suppressible translationalstop codons are the amber, ochre and opal codons.

Mutator Strain

This is a host cell which has a genetic defect which causes DNAreplicated within it to be mutated with respect to its parent DNA.Example mutator strains are NR9046mutD5 and NR9046 mut T1 (see Example38 of WO92/01047).

Helper Phage

This is a phage which is used to infect cells containing a defectivephage genome and which functions to complement the defect. The defectivephage genome can be a phagemid or a phage with some function encodinggene sequences removed. Examples of helper phages are M13K07, M13K07gene III no. 3; and phage displaying or encoding a binding moleculefused to a capsid protein.

Vector

This is a DNA molecule, capable of replication in a host organism, intowhich a gene is inserted to construct a recombinant DNA molecule.

Phage Vector

This is a vector derived by modification of a phage genome, containingan origin of replication for a bacteriophage, but not one for a plasmid.

Phagemid Vector

This is a vector derived by modification of a plasmid genome, containingan origin of replication for a bacteriophage as well as the plasmidorigin of replication.

Secreted

mutations of the sequence desired to be varied. In vivo mutagenesis mayfor example, use mutator strains of hose microorganisms to harbour theDNA (see Example 38 of WO 92/01047). The words “unique population” maybe used to denote a plurality of eg polypeptide chains which are notgenetically diverse, ie they are all the same. A restricted populationis one which is diverse but less so thatn the full repertoire of ananimal or a library, synthetic or otherwise. The diversity may have beenreduced by prior selection, eg using antigen binding specificity.

Domain

A domain is a part of a protein that is folded within itself andindependently of other parts of the same protein and independently of acomplementary binding member. A folded unit is a specific combination ofa α-helix and/or β-sheet structure. Domains and folded units containstructures that bring together amino acids that are not adjacent in theprimary structure.

Free Form

This describes the state of a polypeptide which is not displayed by areplicable genetic display package.

Conditionally Defective

This describes a gene which expresses a defective polypeptide under oneset of conditions, but expresses a different but related non-defectivepolypeptide under another set of conditions. An example, is a genecontaining an amber mutation expressed in non-suppressing or suppressinghosts respectively.

Alternatively, a gene may express a protein which is defective under oneset of conditions, but not under another set. An example is a gene witha temperature sensitive mutation.

Suppressible Translational Stop Codon

This describes a codon which allows the translation This describes argdp or molecule that associates with the member of a sbp displayed onthe rgdp, in which the sbp member and/or the molecule, have been foldedand the package assembled externally to the cellular cytosol.

Repertoire of Rearranged Immunoglobulin Genes

A collection of naturally occurring nucleotides eg DNA sequences whichencoded expressed immunoglobulin genes in an animal. The sequences aregenerated by the in vivo rearrangement of eg V, D and J segments for Hchains and eg the V and J segments for L chains. Alternatively thesequences may be generated from a cell line immunised in vitro and inwhich the rearrangement in response to immunisation occursintracellularly.

Library

A collection of nucleotides eg DNA sequences within clones; or agenetically diverse collection of polypeptides, or specific binding pairmembers, or polypeptides or sbp members which are displayed on rgdpscapable of being selected or screened to provide an Individualpolypeptide or sbp member or a mixed population of polypeptides or sbpmembers.

Repertoire of Artificially Rearranged Immunoglobulin Genes

A collection of nucleotides eg DNA sequences derived wholly or partlyfrom a source other than the rearranged immunoglobulin sequences from ananimal. This may include for example, DNA sequences encoding VH domainsby combining unrearranged V segments with D and J segments and DNAsequences encoding VL domains by combining V and J segments.

Part or all of the DNA sequences may be derived by oligonucleotidesynthesis.

Secretory Leader Peptide

This is a sequence of amino acids joined to the N-terminal end of apolypeptide and which directs movement of the polypeptide out of thecytosol.

Eluant

This is a solution used to breakdown the linkage between two molecules.The linkage can be a non-covalent or covalent bond(s). The two moleculescan be members of a sbp.

Derivative

This is a polypeptide which derived from another polypeptide which isencoded by the DNA within a selected rdgp. The derivative polypeptidemay differ from the encoded polypeptide by the addition, deletion,substitution or insertion of amino acids, or by the linkage of othermolecules to the encoded polypeptide. These changes may be made at thenucleotide or protein level. For example the encoded polypeptide may bea Fab fragment which is then linked to an Fc tail from another source.Alternatively markers such as enzymes, fluoresceins etc may be linked toe.g. Fab, scFv fragments.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows an analysis by ELISA of the specificities of solublesingle-chain Fvs (scFvs) isolated from the unimmunised library byselection on bovine thyroglobulin (upper panel), human TNFα (centralpanel), or the human mAb Fog-1 (gamma-1, kappa). Binding was determinedby ELISA to a panel of proteins, as follows: 1—plastic; 2—hen eggtrypsin inhibitor; 3—chymotrypsinogen A; 4—hen egg ovalbumin; 5—keyholelimpet haemocyanin; 6—bovine thyroglobulin; 7—human TNFα; 8'turkeyegg-white lysozyme; 9—horse heart cytochrome c; 10—bovine serum albumin;11—mAb Fog-1.

FIG. 2 shows an analysis by ELISA of the specificities of soluble scFvsisolated from the unimmunised library by selection on humancarcinoembryonic antigen (CEA) (upper panel), the MUC1 peptide (Price etal., 1990, supra) (central panel), or human CD4 (lower panel). Bindingwas determined by ELISA to a pan l of proteins, as follows: 1—hen eggtrypsin inhibitor; 2—chymotrypsinogen A; 3—hen egg ovalbumin; 4—keyholelimpet haemocyanin; 5—CEA; 6—urine extract containing human polymorphicepithelial mucin (PEM); 7—bovine thyroglobulin; 8—hen egg-whitelysozyme; 9—bovine serum albumin; 10—chicken gamma globulin coupled to4-hydroxy-3-nitrophenyl acetic acid; 11—human recombinant soluble CD4.

FIG. 3 shows an ELISA to assay the binding of three scFvs, isolated byselection on a human monoclonal antibody Fog-1 (IgG1, kappa), to a panelof human antibodies of varying isotype, as follows: 1—Fog-1; 2—the Fvfragment of Hulysll; 3—Hulysll antibody (IgG1, kappa); 4—RegA (IgG1,kappa); FogC (IgG3, kappa); 6—Pag1 (IgG1, lambda); 7 IgG2, lambdaantibody purified from myeloma plasma (Sigma); 8—Oak3 (IgG3, lambda);9—IgG4, lambda purified from myeloma plasma (Sigma); 10 Fom1 (IgM,lambda); 11—FomA (IgM, lambda).

FIG. 4 illustrates the assembly of V_(H) genes in the creation of asynthetic library.

FIG. 5 shows schematically selection techniques for pAbs: 2(i) shows abinding/elution system; 2(ii) shows a competition system (p=pAb;ag=antigen to which binding by pAb is required; c=competitor populatione.g. antibody, pAb, ligand; s=substrate (e.g. plastic beads etc);d=detection system).

The present invention is illustrated by the following examples.Oligonucleotide primers and probes mentioned in the text are listed inTable IV. Tables I to IV are found after Example 8.

Example 1 shows the isolation of antibodies directed against humantumour necrosis factor-α and a human monoclonal antibody from a phagelibrary of single chain Fv fragments derived from an unimmunized human.

Example 2 shows the isolation of antibodies binding to humanthyroglobulin from a phage library of single chain Fv fragments derivedfrom an unimmunized human.

Example 3 shows the isolation of antibody fragments directed against theself antigens MUC1 mucin, carcinoembryonic antigen (CEA) and recombinantsoluble CD4 (rsCD4) from a phage display library of single chain Fvfragments derived from an unimmunized human.

Example 4 shows the further characterization of selected anti-selfantibody fragments by DNA sequencing and affinity determinations.

Example 5 shows the creation of a synthetic human library using germline VH segments.

Example 6 shows the isolation of an antibody fragment binding to humantumour necrosis factor-α from a human germ line synthetic library.

Example 7 shows the creation of a synthetic human library using humangerm line VH segments containing VH CDR3 sequences of different lengthsand isolation of single chain Fv fragments binding to humanthyroglobulin and a human monoclonal antibody.

Example 8 shows the isolation of human antibodies directed against humaninterleukin-1 receptor molecules which trigger receptor function.

EXAMPLE 1 Isolation of Antibody Fragments Directed Against Self Antigensfrom a Library of scFvs Made from Unimmunized Blood Donors

Naturally occuring V-genes isolated from human PBLs can be constructedinto a large library of antibody fragments which contain reactivitiesagainst antigens to which the donor has not been exposed (WO92/01047example 42). We have realised that these libraries may also containreactivities against self antigens, arising either from self-reactiveB-cells which have not been deleted or as non-naturally occuringfragments resulting from VH and VL chain recombination. To test this, wepanned a large human scFv library displayed on the surface of a phagemidagainst human TNF-a and a human IgG/k immunoglobulin.

Methods

Rescue of the Library:

The library of scFvs was constructed from the RNA of human PBLs and hasbeen previously described (WO92/01047 example 42). To rescue phagedisplaying antibody fragments, approximately 10⁹ E. coli harbouring thephagemid were used to inoculate 50 ml of 2× TY containing 1% glucose and100 mg/ml of ampicillin (2× TY-AMP-GLU) and crown to an O.D. of 0.8 withshaking. Five ml of this culture was used to innoculate 50 ml of 2×TY-AMP-GLU, 2×10⁸ TU of delta gene 3 helper (M13 D gene III seeWO92/01047) were added and the culture incubated at 37° C. for 45minutes without shaking and then at 37° C. for 45 minutes with shaking.The culture was centrifuged at 4000 r.p.m. for 10 min. and the pelletresuspended in 2 litres of of 2× TY containing 100 mg/ml ampicillin and50 mg/ml kanamycin and grown overnight. Phage were prepared aspreviously described (WO92/01047 example 42). M13 D gene III wasprepared as follows:

M13 D gene III helper phage does not encode gene III protein, hence thephage(mid) displaying antibody fragments have a greater avidity ofbinding to antigen. Infectious M13 D gene III particles are made bygrowing the helper phage in cells harbouring a pUC19 derivativesupplying the wild type gIII protein during phage morphogenesis. Theculture was incubated for 1 hour at 37° C. without shaking and then fora further hour at 37° C. with shaking. Cells were spun down (IEC-Centra8, 4000 revs/min for 10 min), resuspended in 300 ml 2× TY brothcontaining 100 mg ampicillin/ml and 25 mg kanamycin/ml (2× TY-AMP-KAN)and grown overnight, shaking at 37° C. Phage particles were purified andconcentrated from the culture medium by two PEG-precipitations (Sambrooket al., 1990), resuspended in 2 ml PBS and passed through a 0.45 mmfilter (Minisart NML; Sartorius) to give a final concentration ofapproximately 10¹³ transducing units/ml (ampicillin-resistant clones).

Panning of the Library:

Immunotubes (Nunc) were coated overnight in PBS with 4 ml of either 100mg/ml or 10 mg/ml of recombinant human TNF-a in PBS or 4 ml of 10 mg/mlof Fog-1, a human IgG/k immunoglobulin which recognizes the human redblood cell Rh (D) antigen. Tubes were blocked with 2% Marvel-PBS for 2hours at 37° C. and then washed 3 times in PBS. Approximately 1013 TU ofphage was applied to the tube and incubated for 30 minutes at roomtemperature tumbling on an over and under turntable and then left tostand for another 1.5 hours. Tubes were washed 10 times with PBS 0.1%Tween-20 and 10 times with PBS. Phage were eluted by adding 1 ml of 100mM triethylamine and rotating 15 minutes on an under and over turntableafter which the solution was immediately neutralized with 0.5 ml of 1,0M Tris-HCl, pH 7.4. Phage were then used to infect 10 ml of mid-log E.coli TG1 by incubating eluted phage with bacteria for 30 minutes at 37°C. The E. coli were then plated on TYE plates containing 1% glucose and100 mg/ml ampicillin. The resulting bacterial library was then rescuedwith delta gene 3 helper phage as described above to prepare phage for asubsequent round of selection. This process was then repeated for atotal of 4 rounds of affinity purification with tube-washing increasedto 20 times with PBS, 0.1% Tween-20 and 20 times with PBS for rounds 3and 4.

Characterization of Binders:

Eluted phage from the 3rd and 4th rounds of selection were used toinfect E. coli HB 2151 and soluble scFv was produced (Marks, et al.,1991) from single colonies for assay. In the case of TNF, phage was alsorescued from single colonies. ELISAs were performed as previouslydescribed with microtitre plates coated with either 10 μg/ml human TNF-ain 50 mM bicarbonate pH 9.6 or 10 μg/ml Fog-1 in PBS. Clones positive inELISA were further characterized by PCR fingerprinting (WO92/01047example 20) and then by sequencing.

Results

TNF: Soluble scFv from 1536 colonies and phage from 1152 colonies werescreened by ELISA. The results are shown in FIG. 1, the key for which isgiven in the brief description of the figures (supra). Positive clonesfor binding to TNF-a were further characterized by PCR fingerprintingand sequencing. In this manner, 15 different binders were identified.Four of these have been sequenced.

Fog-1: Soluble scFv from 96 clones was screened by ELISA and positiveclones were further characterized by PCR fingerprinting and sequencing.In this manner, four different binders were identifed and sequenced.

EXAMPLE 2 Isolation of Antibody Fragments Specificities Directed AgainstHuman Thyroglobulin from a Library of scFv Fragments Using Display onBacteriophage fd

Example 44 of WO92/01047 describes the selection of antibody scFvfragments directed against bovine thyroglobulin from a library of scFvfragments. These were derived from unimmunised humans, expressed on thesurface of phage fd, isolated by panning against bovine thyroglobulin.The results demonstrated that it is possible to isolate from a libraryderived from an unimmunised individual antibody fragments which willbind an antigen to which that individual has never been exposed.

Sixteen clones found by this panning to be specific for bovinethyroglobulin have now been analysed for binding to human thyroglobulinin an ELISA assay (as described in example 44 of WO92/01047). Nine ofthese clones also bound strongly to human thyroglobulin with absorbancesignals of between 1.0 and 1.6 12 minutes after addition of substrate.No cross-reactivity (signal less than 0.05 after 90 min) was found witha panel of unrelated antigens—hen egg lysozyme, BSA, ovalbumin,chymotrypsinogen, cytochrome c, keyhole limpet hemocyanin, insulin,cardiolipin and DNA.

Thus, antibodies with specificity for epitopes on the human self antigenthyroglobulin can be isolated from libraries prepared from unimmunisedhumans.

Two clones binding to both human and bovine thyroglobulin, α-Thy23 andα-Thy29, and two clones binding to bovine thyroglobulin only α-Thy32 andα-Thy33, were sequenced.

EXAMPLE 3 Isolation of Antibody Fragments Directed Against the HumanSelf-Antigens MUC1Mucin, Carcinoembryonic Antigen (CEA) and RecombinantSoluble CD4 (rsCD4) from a Phage Display Library of Human Single ChainFv Fragments

The phage display library of single chain Fv fragments derived fromunimmunized human donors used in Example 1 was used in selection toisolate antibody fragments directed against the self-antigens MUC1mucin, carcinoembryonic antigen (CEA) and recombinant soluble CD4(rsCD4).

Rescue of the Library

The library was rescued as in example 1 except that the standard helperphage M13K07 (5×10¹⁰ pfu) was used to rescue the library rather thandelta gene 3 helper phage (M13 D gene III).

Selection of Phage Specific for MUC1 Mucin and Carcinoembryonic Antigen(CEA)

The phage were panned for binding using immuno tubes (Nunc; Maxisorp)coated with antigen essentially as (Marks et al., 1991), or wereselected on a column of antigen (J. McCafferty et al., Nature 348552-554, 1990). The following antigens were used: human recombinantsoluble CD4 (rsCD4) (expressed in baculovirus by AmericanBiotechnologies Inc. and supplied by the MRC AIDS Reagent Project[ADP608]); human carcinoembryonic antigen (CEA); and a 20 amino acidpeptide (M. R. Price et al., Molec. Immunol. 27 795-802, 1990), whichcorresponds to a repeated motif in human MUC1 mucin (tumour-associatedpolymorphic epithelial mucin or PEM) (S. Gendler et al., J. Biol. Chem.263 12820-12823, 1988; J. R. Gum et al., Biochem. Biophys. Res. Commun.171 407-415, 1990).

CEA (20 mg/ml) and rsCD4 (10 mg/ml) were coated on immunotubes overnightat room temperature in phosphate buffered saline. For the first tworounds of selection tubes were washed 10 times with PBS, 0.1% (v/v)Tween 20 and 10 times with PBS. For subsequent rounds of selection tubeswere washed 20 times with PBS, 0.1% (v/v) Tween 20 and 20 times withPBS. Phage were eluted with 100 mM triethylamine as (Marks et al.,1991). Eluted phage (usually 10⁶ to 10⁷ transducing units) were used toinfect E. coli TG1 cells. Approx. 10⁹ infected bacteria were used as aninoculum for the next rescue.

The library was subjected to 3 to 5 rounds of rescue and selection foreach antigen.

For selection of phage binding to the MUC1 peptide, the peptide wascoupled chemically to Sepharose 4B (provided by M. R. Price). A 1 mlcolumn was prepared, and phage was selected as described by McCaffertyet al., 1990 (supra). Briefly, the Sepharose-MUC1 column was washed withPBS containing 2% skimmed milk powder (MPBS) and the phage loaded in 1ml of the same buffer. After washing the column successively with 10 mlvolumes of MPBS, PBS pH7.2, 50 mM Tris-HCl/500 mM NaCl pH8.0, and 50 mMTris-HCl/500 mM NaCl pH9.0, phage was eluted with 5 ml 100 mMtriethylamine and neutralised with 0.5M sodium phosphate buffer pH 6.8.Five rounds of selection were carried out.

Screening and Sequencing of Clones

Single ampicillin resistant colonies from infection of E. coli TG1 witheluted phage, were screened either for binding of phage (Clackson etal., 1991) or soluble scFv fragments (Marks et al., 1991). Since thegene encoding the antibody fragment is linked to that encoding the phagecoat protein by an amber codon, soluble fragments can be secreted from anon-suppressor strain of bacteria infected by the phage (Hoogenboom etal., 1991). The binding to antigen of soluble scFvs in bacterialsupernatant was detected with the mouse mAb 9E10 (1 μg/ml), whichrecognises the C-terminal peptide tag (Munro and Pelham, Cell 46,291-300, 1986), and peroxidase-conjugated anti-mouse Fc antibody(Sigma), as described (Ward et al., 1989). Plates were coated with theantigens Fog1, TNFa, bovine thyroglobulin and rsCD4 as described forimmuno tubes above, and with CEA at 5 mg/ml. A urine extract containinghuman polymorphic epithelial mucin (PEM) was used at a proteinconcentration of approximately 10 mg/ml.

The specificity of the isolated clones was checked by ELISA of thesoluble scFv fragments using plates coated with various proteins. Plateswere coated with the antigens Fog-1, TNFa, bovine thyroglobulin, rsCD4,CEA and PEM as described above. Other proteins were coated overnight atroom temperature at a concentration of 1 mg/ml in PBS (cytochrome c[Sigma]) or in 50 mM NaHCO3, pH 9.6 (bovine serum albumin, turkeyegg-white lysozyme, hen-egg-white lysozyme, hen ovalbumin, keyholelimpet haemocyanin [CalBiochem], chymotrypsinogen A, chicken egg-whitetrypsin inhibitor [Sigma], chicken gamma globulin coupled to4-hydroxy-3-nitrophenyl acetic acid. Clones found to give a positiveELISA signal were screened by PCR and ‘fingerprinted’ with therestriction enzyme BstNI as in (Marks et al., 1991, supra) to identifydifferent clones. Examples of clones with different restriction patternswere selected and the heavy and light chains sequenced using a Sequenasekit (USB) or using a Taq DyeDeoxy Terminator Cycle Sequencing kit(Applied Biosystems) and an Applied Biosystems 373A DNA sequencer.

Sequenced clones were further analysed using the program MacVector 3.5(IBS Kodak, New Haven, Conn.). The VH genes were compared to the 83germline gene segments present in the VH directory compiled by Tomlinsonet al. (J. Mol. Biol. 227 776-798, 1992). VL genes were compared with 34published kappa germline gene segments and 13 published lambda genesegments. Regions of the V-genes encoded by PCR primers were notincluded in the analysis.

The Selected Human Antibody Fragments Show High Specificity AgainstSelf-Antigens

After two to five rounds of selection, E. coli cells were infected witheluted phage and antibody fragments produced by individual clones werescreened for binding by ELISA. Phage selected with the 20 amino acidMUC1 peptide (Price et al., 1990, supra), which corresponds to arepeated motif in human MUC1 mucin (tumour-associated polymorphicepithelial mucin or PEM) (Gendler et al., 1988, supra; Gum et al., 1990,supra), were screened for binding to human PEM and hence bind to bothpeptide and the protein. The V-genes of clones with binding activitieswere sequenced, and one clone identified for each antigen of CEA, PEMand rsCD4 (Table I). The appearance of only low numbers of clonesbinding to CEA, PEM and human recombinant soluble CD4 (rsCD4), evenafter several rounds of selection, may reflect the use of VCS-M13(stratagene) as helper phage (instead of M13DgIII helper used for theother antigens). Populations of phage(mid) particles produced by rescuewith M13DgIII (which cannot produce pIII) have higher average aviditiesthan those produced by rescue with VCS-M13 (where the wild-type pIIIencoded by the helper phage can compete with scFv-pIII fusions).

The scFv fragments were then screened for binding to a panel of otherprotein antigens, and were found to be highly specific. This isillustrated in FIG. 2 with the single clones with binding activity tohuman CEA, MUC1 and human rsCD4. See brief description of FIG. 2 (supra)for key.

Hence, antibody fragments directed against the human self antigens CEAand MUC1 which are tumour markers) and rsCD4 can be derived from thesame library and they all have a high specificity for antigen.

EXAMPLE 4

Characterisation of Antiself Antibody Fragments by DNA Sequencing andBinding to Antigen

The antiself antibody fragments isolated in examples 1,2 and 3 werecharacterized by DNA sequencing and antigen binding.

The Antibody Fragments are Derived from a Range of Unmutated andSomatically Mutated V-genes

The sequences of several clones with self-specificity were determined asin example 3 and contain both kappa and lambda light chains (Table II).Comparison with the sequences of the nearest germ-line V-gene segmentsindicates that several different families are used (VH1, 3, 4 and 5; Vk1and 4, Vl1, 2 and 3). In a few cases the V-genes are completelygermline, for example both the VH and Vl genes of aThy-29. However, mostof the V-genes have several differences from the nearest germline V-genesegments, both at the nucleotide and amino-acid level (Table II),suggesting that they are derived from somatically mutated B-cells. Somemutations may have arisen during the PCR amplification and assemblyprocess, for example the VH-genes of aFOG1-G8 and aMUC1-1, and theVk-gene of aThy-33 probably arose from cross-overs between two V-genesduring PCR amplification (Table II). Furthermore, large differences (forexample the Vk of aFOG1-H6 which differs by 36 nucleotides) may be dueto the use of unknown V-gene segments. There is a striking homology inthe CDR3 of the heavy chain between aTNF-A1 and aTNF-E1: the germlineV-genes are different but the same JH segments are used, and 11/16residues of CDR3 are identical. This suggests that both scFv fragmentsmay bind to the same epitope of TNF.

The Antibody Fragments are Directed to Different Epitopes on the SameProtein

The scFv fragments directed against bovine thyroglobulin from example 2were screened for binding to human thyroglobulin, which differs by only6 single amino-acid residues in the protomer (Malthiéry, Y. andLissitzky, S. (1987) Eur. J. Biochem., 165, 491-498). Four of the twelveclones (including aThy-29) bound to human thyroglobulin, whereas therest (including aThy-32 and aThy-33) did not (data not shown). Likewisethe fragments binding to the human antibody Fog-1 were screened forbinding to a range of other antibodies differing in heavy and lightchain isotype (FIG. 3). See brief description of FIG. 3 for its key(supra). The fragment aFOG1-A4 bound to all heavy chain g1, 2 and 3isotypes, but not to g4 or m. By contrast, the fragments aFOG1-H6 andaFOG1-A3 did not bind to any of the other antibodies, including those ofthe same isotype as Fog-1, suggesting that they are directed to thevariable domain of Fog-1.

Characterisation of Selected scFv Fragments

The following clones were chosen for large scale purification andfurther characterisation: aFOG1-H6, aFOG1-A3, aTNF-E7, and aThy-29.Colonies of the non-suppressor E. coli strain HB2151 harbouring theappropriate phagemid were used to inoculate 2 litres of 2× TY containing100 μg ampicillin/ml and 0.1% glucose. The cultures were grown andinduced (De Bellis, D. and Schwartz, I. (1990) Nucleic Acids Res., 18,1311) and the tagged scFv fragments purified using the mAb 9E10 as in(Clackson et al., 1991, supra and WO92/01047).

The inhibition of 125I-Fog-1 binding to human Rh D antigen by theaffinity purified scFv fragments aFOG1-H6 and aFOG1-A3 was essentiallyas performed earlier (Gorick, B. D., Thompson, K. M., Melamed, M. D. andHughes, J. N. (1988) Vox. Sang., 55, 165-170) with the followingmodifications. 0.0148 μg of 125I-FOG1 was pre-incubated with varyingamounts of purified aFOG1-H6 or aFOG1-A3 scFv fragments (0-16 μg) at 37°C. for 1.5 hours, before adding 0.5 μl of R1R2 cells (or rr cells ascontrol). The mixture was then incubated for a further 1.5 hours at 37°C. with constant mixing, and finally cells separated from thesupernatant. As a control, a titration was also performed with apurified scFv fragment directed against turkey egg white lysozyme(aTEL9) (Marks et al., 1991, supra).

Kinetic measurements were made using surface plasmon resonance (BIAcore,Pharmacia Biosensor AB) (J{umlaut over (n)}onsson, U., Fägerstam, L.,Ivarsson, B., Lundh, K., Löf{dot over (a)}s, S., Persson, B., Roos, H.,Rönnberg, I., Sjölander, S., Stenberg, E., St{dot over (a)}hlberg, R.,Urbaniczky, C., Östlin, H. and Malmqvist, M. (1991) BioTechniques, 11,620-627; Jönsson, U. and Malmqvist, M. (1992) In Turner, A. (ed.), RealTime Biospecific Interaction. JAI Press Ltd., San Diego, Vol. 2, pp.291-336). In order to separate monomeric and multimeric species, thepurified scFv fragments were concentrated by ultrafiltration and thenfractionated on a calibrated Superdex 75 FPLC column (Pharmacia) in PBS,0.2 mM EDTA. Gel filtration was monitored both by the absorbance at 280nm and on-line to BIAcore with immobilised antigen on the sensor chip(Johnsson et al., 1991).

Kinetic experiments were performed in two different configurations.First, to analyse the binding of soluble scFv, the different antigenswere covalently immobilised on the sensor chip (in the case of mAbFog-1, the antibody was also immobilised via a mouse anti-human kappalight chain mAb using a sensor chip coated with rabbit anti-mouse IgG1).Second, to analyse the binding of the soluble mAb FOG-1, the aFOG1-H6scFv was immobilised on the chip surface.

The antigens were coupled to the CM5 sensor chip through their aminegroups using the Amine Coupling Kit (Pharmacia Biosensor AB)(Johnsson,B., Löf{dot over (a)}s, S. and Lindqvist, G. (1991) Anal. Biochem., 198,268-277). The antigens were diluted in 10 mM acetate buffer pH 5.0 toapprox. 25 μg/ml, and 3805 resonance units (RU) of TNF, 6249 RU of humanthyroglobulin, and 5279 RU of FOG1 were immobilised. For the biospecificpresentation of Fog-1, affinity purified rabbit anti-mouse IgG1(Pharmacia Biosensor AB) was coupled to the surface followed by a mousemAb anti-human kappa (2300 RU) and then Fog-1 (2050 RU). As binding ofthe rabbit anti-mouse IgG1 to the mouse mAb was reversible by 10 mM HClthe complex was rebuilt for each analytical cycle. ScFv anti-Fog-1 wascoupled to the CM5 surface to 1538 RU. All determinations were performedat 25° C. in PBS, 0.2 mM EDTA, 0.05% BIAcore surfactant P20 with aconstant flow-rate of 10 μl/min. and an injected volume sample of 35 μl.It was not necessary to regenerate the antigen as the scFv fragmentsrapidly dissociate, with the exception of the biospecific presentationof antigen via rabbit anti-mouse IgG1 which was regenerated with 10 mMHCl for 3 min.

Analyses of scFv monomer were performed in the concentration range100-500 nM, and dimers in the range 40-200 nM except for thebiospecifically presented Fog-1 where the concentration of dimeric scFvwas 0.25-1.26 μM. Fog-1 was analysed on the aFOG1-H6 scFv surface in theconcentration range 10-200 nM. All concentrations were calculated fromU.V. absorption at 280 nm (assuming that 0.7 mg/ml scFv gives an A280=1[Mach, H., Middaugh, C. R. and Lewis, R. V. (1992) Anal. Biochem., 200,74-80], and that Mr of a scFv monomer is 30 kD and of a dimer is 60 kD).No correction was made for the fraction of active protein, and thereforethe on-rates are an underestimate. The kinetic evaluation of data wasperformed according to (Karlsson, R., Michaelsson, A. and Mattsson, L.(1991) J. Immunol. Methods, 145, 229-240) and evaluated on the programOrigin 1.1 (Microcal inc., Northampton, Mass., USA).

Two of the Antibody Fragments are Directed Against Idiotopes of HumanmAb Fog-1

The binding of 125I-Fog-1 antibody to human red blood cells bearing theRh D antigen could be inhibited by both aFOG1-H6 and aFOG1-A3 scFvfragments. Hence, both aFOG1-H6 and aFOG1-A3 are site-associatedanti-idiotype antibodies, complexing with the antigen-binding site ofFog-1. The extent of inhibition of 125I-Fog-1 binding to the Rh Dantigen (on human R1R2 red blood cells) was determined by titration withaffinity purified aFOG1-H6 and aFOG1-A3 scFv fragments. (As control, noinhibition of 125I-Fog-1 binding was observed using a scFv fragment(aTEL9) (Marks et al., 1991, supra) directed against turkey egg whitelysozyme). With the maximum of 16 μg scFv (1000 fold molar excess to125I-Fog-1), the binding was inhibited by 14.2% (aFOG1-H6) and 20.9%(aFOG1-A3), suggesting that the affinities of these fragments for Fog-1are much lower than the affinity of Fog-1 for the Rh D antigen(Ka=2.2×10⁹ M⁻¹) which binds monovalently (Gorick et al., 1988, supra).If 100% of the fragments are active, the affinities of the two fragmentsfor binding to Fog-1 could be estimated as Ka=3×10⁵ M⁻¹ for aFOG1-H6 and6×10⁵ M⁻¹ for aFOG1-A3, and this is consistent with other kineticmeasurements (see below and Table III).

The scFv Fragments Can form Both Monomers and Dimers in Solution

Soluble antibody fragments were purified from bacterial supernatants byaffinity chromatography, by binding of -he C-terminal peptide tag to themAb 9E10. After ultrafiltration, the fragments were further purified byFPLC gel filtration (Pharmacia) on Superdex 75 (Pharmacia), and detectedon-line both by UV absorption (280 nm) and by binding to antigenimmobilised on a sensor chip in BIAcore (Pharmacia Biosensor ABS. Thisshowed that the scFv fragments emerged in two peaks, corresponding insize to monomers and dimers. The dimers bind more strongly to theimmobilised antigen than monomers due to their greater avidity ofbinding. The scFv dimers run as monomers on non-reducing SDS gels, andare therefore not linked by disulphide bonds. As two peaks are seen ingel-filtration, it appears that in this case the monomers and dimers donot interconvert rapidly. Presumably the dimers are scFv fragmentsinterlocked through the flexible linker joining the heavy and lightchains, or with the heavy chain of one scFv molecule associated with thelight chain of the other. We note that antibody Fab fragments made inbacteria can also multimerize (unpublished data).

The scFv Fragments have Micromolar Affinities

The presence of both scFv monomers and dimers could lead to anoverestimate of affinity of binding using solid phase methods. Todetermine the affinity and kinetics of binding of scFv fragments to theantigen coated chip using surface plasmon resonance, we thereforepurified the fragments by gel filtration (Table III). For the dimers,the off-rate constants were determined as about 10⁻² s⁻¹ and the on-rateconstants for the scFv dimers as about 10⁵-10⁶ M⁻¹ s⁻¹ (assuming thesample is completely active). In the ease of aFOG1-H6, the antigen (themAb Fog-1) was immobilised on the sensor chip in two ways, eitherdirectly or via a rabbit anti-mouse IgG1 antibody. The results werealmost identical by either method (see Table III). However the activefraction of scFv fragments varies considerably and could lead to anunderestimate of the on-rate (and affinity of binding); for exampleusing fluorescence quench titration with several scFv fragments directedagainst phenyloxazolone we detected only 0.06 to 0.38 functional bindingsites per scFv molecule (unpublished data). Indeed the on-rate constantscalculated for the association of the aFOG1-H6 fragment and Fog-1antibody depend on whether the antibody (k_(on) 2.2×10⁵ M⁻¹ s⁻¹) or scFvfragment (k_(on) 1.0×10⁶ M⁻¹ s⁻¹) is immobilised on the sensor chip(Table III), indicating that the aFOG1-H6 fragment is less active thanthe Fog-1 antibody. For the scFv monomers, the binding signals were lowand it was difficult to follow the kinetics of binding to the surface,except for the dissociation of the aThy-29 monomer (k_(off)=2×10⁻² s⁻¹).However, the four fold stabilisation of the aThy-29 fragment dimer (seebelow), suggests that the off-rate constants of the other monomers are>10⁻² s⁻¹, perhaps 10⁻¹ s⁻¹.

The greater stability of the scFv dimers on the sensor chip, compared tomonomers, indicates that the diners are bivalent. The scFv dimers aretherefore analogous to the two heads of the antibody IgG (but withdifferent spacing between the heads), and their binding avidities wereestimated as about 10⁷ M⁻¹ from k_(on)/k_(off) (Table III). Theaffinities of the monomers must be lower by virtue of their fasterdissociation from the surface. For the aThy-29 monomer, and assumingthat the on-rate constant is the same as for the dimer (Mason, D. W. andWilliams, A. F. (1986) Kinetics of Antibody Reactions and the Analysisof Cell Surface Antigens. Blackwell Scientific, Oxford), we can estimatean affinity of about 3×10⁶ M⁻¹. These affinities, calculated from therate constants measured by surface plasmon resonance appear to besimilar to those measured in solution by fluorescence quench techniques.For example the affinity of binding of the monomer scFv fragment aTEL9(Marks et al., 1991) which binds to turkey lysozyme (and was derivedfrom the same library) was estimated as 3.9×10⁷ M⁻¹ using surfaceplasmon resonance (Table III), and as 1.2×10⁷ M⁻¹ by fluorescence quench(Marks et al., 1991, supra).

The affinities of antibodies isolated are typical of antibodies from themouse primary immune response (Foote, J. and Milstein, C. (1991) Nature,352, 530-532). The kinetics of association of the antibody fragments tothe protein self-antigens (10⁵ to 10⁶ M⁻¹ s⁻¹) are also typical ofpreviously characterised Ab-protein interactions. However the kineticsof dissociation (10⁻² s⁻¹) are relatively fast for Ab-proteininteractions (but both rates are slow compared to many Ab-hapteninteractions). At first sight, it is surprising that we can isolate scFvfragments with such fast off-rates, as one would not expect a“monomeric” phage to be retained on the solid support during washing.However, scFv fragments are displayed multivalently on the phage,especially using the M13DgIII helper phage, and some of the scFvs whichtend to form dimers in solution, may also form dimers on phage. Themultivalent interactions with antigen help retain the phage, allowingthe encoded scFv phage to be isolated.

Random combinatorial V-gene repertoires derived from the mRNA ofimmunised animals are enriched for heavy or light chain V-genes encodingpart of an antigen binding site and this facilitates the isolation ofantigen-binding fragments using phage technology, although thecombinations of V-genes of each B-lymphocyte appear to be largelydestroyed. Antigen binding sites can also be generated de novo by therandom combination of chains, as illustrated by the isolation of scFvfragments against foreign antigens from unimmunised human donors (Markset al., 1991, supra).

“Natural autoantibodies”, self-reactive antibodies isolated from healthydonors tend to be of low affinity and polyspecific and may well beproduced by a discrete subset of B-cells, the internal activity set(Holmberg, D. and Coutinho, A. (1985) Immunol. Today, 6, 356-357),contributed in part by CD5+ B-cells (Casali, P. and Notkins, A. L.(1989) Annu. Rev. Immunol., 7, 513-535). In contrast, the anti-self scFvfragments we have made are highly specific in binding to antigen despiteonly having micromolar affinities. This is a surprising and valuablefinding. Their affinities could presumably be improved in vitro, forexample, the affinity of an scFv fragment for the hapten phenyloxazolonederived from the phage library (and, like the anti-self antibodiesdescribed here, with a relatively fast off-rate) was improved fromKa=3.1×10⁶ M⁻¹ to 9.1×10⁸ M⁻¹ by chain shuffling (WO92/01047; Marks etal., 1992b, Biotechnology 10, 779-783, 1992). This would allow thecreation of highly specific, high affinity human antibodies directedagainst self-antigens for use in human therapy.

EXAMPLE 5

Creation of a Synthetic Library

By display of antibody repertoires on the surface of filamentous phageand selection of the phage with antigen¹, we can mimic immuneselection^(2,3) and make human antibodies from the rearranged V-genes ofunimmunised donors⁴. Human antibodies have now been made by synthesisfrom defined V-gene elements. A repertoire of 49 human germ line V_(H)gene segments was rearranged in vitro by joining to a synthetic“D-segment” of five random amino acid residues and a J-segment, tocreate a synthetic third complementarity determining region (CDR) ofeight residues. The rearranged V_(H) genes were cloned with a humanVlambda3 light chain as single-chain Fv fragments for phage display. Thelibrary of 10⁷ phages was panned with a hapten 2-phenyl-oxazol-5-one(phOx) conjugate to bovine serum albumen (BSA), and phage isolated thatencoded fragments with specific binding activity to phOx-BSA, and withaffinities to phOx-gamma-aminobutyric acid (phOx-GABA) in the micromolarrange. Comparison of twenty one clones with unique sequences showed thatthe in vitro “immune response” to the hapten was largely restricted tothe V_(H)26 segment (V_(H)3 family)⁶ with an invariant aromatic residue(Tyr, Phe, Trp) at residue 98 of CDR3. The use of V-genes rearranged invitro may allow the design so of antibody libraries biased towards thebinding of antigens of known structure, and the creation of therapeutichuman antibodies with reduced immunogenicity.

Antibody variable domains consist of a β-sheet framework with threeloops of hypervariable sequence or CDRs⁵. The loops create antigenbinding sites of a variety of shapes, ranging from flat surfaces⁷ topockets⁸. For human heavy chains, the sequence diversity of the firsttwo CDRs are encoded by a repertoire of about fifty germ line V_(H)segments. (I. M. Tomlinson et al., supra). The third CDR is generatedfrom the recombination of these segments with about thirty D and six Jsegments⁹, and although its sequence is highly variable, it oftenincludes a salt bridge from Asp101 of the loop to Arg94 of theframework¹⁰. The structures and lengths of the first two CDRs arerestricted^(10,11), but those of CDR3 differ greatly, with lengthsranging from 4 to 25 residues⁵.

A library was created of rearranged V_(H) genes with a CDR3 of eightresidues including Asp101, in combination with a single Vlambda (ref.12)light chain. Forty nine germ line V_(H) segments encoding most of thehuman V_(H) repertoire (Tomlinson et al., supra) were each amplifiedusing the polymerase chain reaction¹³ and oligonucleotide primers thatintroduce a synthetic D-segment (of 15 bases of random sequence at the3′ end of the V_(H) segment) and a J-segment, together encoding a CDR3loop of eight residues (FIG. 4). The rearranged segments were pooled andcloned for phage display with a human Vlambda3 light chain, creating asynthetic library of 10⁷ phage clones. Like the immune system, thesynthetic library of 10⁷ phage clones can tap only a small fraction ofthe potential diversity. Thus the diversity is potentially49×32⁵=1.6×10⁹ different nucleotide sequences, or 49×20⁵=1.6×10⁸different amino acid sequences.

The library was subjected to four rounds of growth and panning onphOx-bovine serum albumin (BSA) coated tubes, and clones screened assoluble¹⁴ single chain Fv fragments15,16 for binding activity tophOx-BSA by ELISA⁴. After the third and fourth rounds, 14/96 and 61/96clones respectively were identified with binding activities to phOx-BSAand of these (29 tested) none bound to other proteins (see legend TableB). Furthermore their binding to phOx-BSA coated plates could becompeted with the soluble hapten (Table B).

Sequencing revealed that many (21/29) of the phOx binders were unique,with an eight residue CDR3, and utilised either a segment from the V_(H)⁴ family, or one of three segments from the V_(H) ³ family (Table B).Together these segments use three of the seven “canonical” foldsavailable to the first two hypervariable loops of human V_(H) segments.(C. Chothia, et al., supra). The majority of the unique clones (16/21)were derived from the VH26 segment⁶ and have related sequences in thethird hypervariable loop: in this group the first residue tends to havea branched aliphatic side chain (15/16), the second residue tends to belysine or arginine (11/16), while the fourth residue is always anaromatic residue (most frequently tyrosine).

The affinities (K_(d)) of two of the stronger binders (Ox 13 and Ox-31,Table B) for phOx-GABA were determined by fluorescence quenchtitration¹⁷ as 3.1±0.2 μM and 6.7±0.7 μM respectively. Although thesynthetic antibody library lacks the diverse VH-CDR3 lengths and thedifferent light chains of antibodies made in vivo, the affinities forphOx-GABA compare with 0.5 μM for a (phage) ant-body made fromunimmunised human donors⁴, or 1 μM for several hybridomas from a mouseprimary immune response¹⁸ (but see caveat, Table A legend). To improvethese affinities, one could systematically alter (see below) the manydifferent phOx antibodies selected (Table A).

In principle, the use of phage display libraries of V-genes rearrangedin vitro offers an attractive alternative to these rearranged in vivo⁴.Firstly the framework regions and first two hypervariable loops of bothheavy and light chains of the synthetic human antibodies created fromthe library are essentially germ line. This contrasts with the “primary”phage antibodies tapped from human V-genes rearranged in vivo, in whichthe extent of somatic mutation varied widely⁴. Leaving asidepolymorphism, the VH gene segments are identical in differentindividuals, and the synthetic antibodies are potentially lessimmunogenic. By altering the lengths and sequences of the heavy andlight chain CDR3 loops, or by localising the minimal mutations in theother CDR loops, or by shuffling with synthetic “germ line” lightchains^(19,20,) it may be possible to improve their affinities whileretaining their germ line character.

Secondly both kinds of libraries are highly biased. In the “natural”libraries, the bias is outside our control, and is imposed for exampleby allelic variation, deletion polymorphism and deletion ofself-reactive clones. In the synthetic library, the bias can beintroduced systematically. Here for example, all the VH-gene segments,were chosen and thereby the folding of the first and secondhypervariable loops: also fixed were the length and diversity of VH-CDR3and the light chain. Although several ways of making diverse syntheticlibraries have been suggested², it should also be possible toincorporate design principles into the encoded structures. If the shapeof the antigen were known, an envelope of roughly complementary bindingsites might be designed and built with defined V-gene elements. Use ofsuch “designer” libraries would favour the isolation of antibodies withhigher affinities. TABLE A No. of Library size Family genes VH segments*×10^(−6 (%)) V_(H)1 14 1-5, 7, 8, 10, 12, 2.3 (20) 14, 15, 20, 21, 25V_(H)2 1 27 1.0 (9)  V_(H)3 23 29-33, 35, 38-40, 2.1 (19) 42, 44-54, 58,59 V_(H)4 9 63-71 2.6 (23) V_(H)5 1 73 1.4 (12) V_(H)6 1 74 1.9 (17)Total: 49 11.3 (100)*for simplicity V_(H) segments are listed according to DP nomenclatureof Tomlinson et al., supra.Table A—Composition of the Synthetic Library

Forty nine human V_(H) segments (Tomlinson et al, supra) were used, onefor each of the V_(H) ², V_(H) ⁵ and V_(H)6 gene families and multiplesegments for the other three families, and cloned according to family.Clones from the V_(H) segments of each family were checked for presenceof insert (on average 85%) and pooled into a single large library as inTable B, creating a (controlled) bias for certain gene families. Thesegments from the V_(H) ², V_(H) ⁵, V_(H) ⁶ families are thereby“overrepresented” with respect to the segments from other families.Sequencing of thirty five clones from the unselected Library confirmedthat V_(H) segments from each family were present, and that thenucleotides were present in the expected ratios in the D-segment, butwith a slight bias for C. (At the first and second position of eachcodon, A, 21.3%; G, 17.9%; C33.7% and T, 27.1%; at the third position,G, 42.6% and T., 57.4%). The expression levels of the antibody fragmentswere also checked, and V_(H) segments were identified in clones withdetectable expression levels, for example V_(H)1 (DP-7), V_(H) ²(DP-27), V_(H) ³ (DP-29,35,38,44,47,51,53), V_(H) ⁴ (DP-63,69), V_(H) ⁵(DP-73) and V_(H) ⁶ (DP-74).

Methods

The clones were checked for presence of insert by ‘PCR-screening’²¹ witholigonucleotides LMB3 and pHEN-SEQ (ref.4) and sequenced fromdouble-stranded DNA by the dideoxy chain termination method²² witholigonucleotide LINKSEQ (5′-CGA TCC GCC ACC GCC AGA G-3′). (The numbersin the tables are corrected for insert). Expression of soluble scFvfragments was checked by spotting 10 μl supernatant of induced overnightcultures in E. coli HB2151 (ref.14) onto a nitrocellulose filter using aslot-blot device (Minifold II, Schleicher and Schuell), and detectingthe bound peptide-tagged scFv fragments with 9E10 antibody²³ andperoxidase labelled anti-mouse antibodies (Sigma). TABLE B GermlineCanonical Loop Clone Family gene* structure* I₅₀ ^(φ) Ox-31 V_(H)3 DP-421-1 26 Ox-15 V_(H)3 DP-45 1-1 >300 Ox-18 ″ ″ ″ >300 Ox-33 V_(H)3 DP-471-3 20 Ox-13 ″ ″ ″ 50 Ox-9 ″ ″ ″ 80 Ox-7 ″ ″ ″ 86 Ox-30 ″ ″ ″ 86 Ox-12 ″″ ″ 86 Ox-5 ″ ″ ″ 100 Ox-3 ″ ″ ″ 125 Ox-20 ″ ″ ″ 125 Ox-21 ″ ″ ″ 125Ox-4 ″ ″ ″ 130 Ox-10 ″ ″ ″ 150 Ox-14 ″ ″ ″ 180 Ox-19 ″ ″ ″ 250 Ox-25 ″ ″″ >400 0x-27 ″ ″ ″ ¶ Ox-2^(§) V_(H)4 DP-67 2-1 >400 Ox-1 ″ ″ ″ >400*Tomlinson et al., supra, Chothia et al., supra.^(φ)in μM, according to competition ELISA with phOx-GABA.^(§)shows V67A mutation in FR3.¶ Not determined.Table B—phOx-binders Isolated from the Synthetic Library

Phage were prepared from the library by rescue with VCS-M13, andsubjected to rounds of panning in phOx-BSA coated tubes as in ref.4. Thesequences of 21 phage binding to phOx revealed four germ line VHsegments, DP-42,45,47 (VH3 family) and DP-67 (VH4 family). DP-47 isidentical to VH26 (ref.6, corrected in ref.24), while DP-42, DP-45 andDP-67 only differ in one or a few framework residues from 8-1B (ref.25),65-2 (ref.26) or VH4.22 (ref.27) respectively. Clones from theunselected library using the DP47 V_(H) segment and lacking thecharacteristic pattern of CDR3 did not bind to phOx. Of the 21 phOxbinders tested, none bound to BSA, NIP-BSA, plastic, chymotrypsinogen A,cytochrome c, bovine thyroglobulin, keyhole limpet haemocyanin or turkeyegg white lysozyme. Four clones that bound to BSA (but not to phOx) werefound to be contaminants (αBSA3 clones, from ref.4).

Methods

As in ref.4. The relative affinities of the scFv fragments weredetermined by inhibition ELISA²⁸. A serial dilution of4-gamma-amino-butyric acid methylene 2-phenyl-oxazol-5-one (phOx-GABA),with concentrations ranging from 6 to 400 μM, was made in 4% Marvel-PBS,and scFv supernatant added. The concentration of phOx-GABA resulting ina 50% reduction of the signal (I₅₀) for binding to phOx-BSA was noted.The affinities of the clones Ox-13 and Ox-31 for phOx-GABA weredetermined by fluorescence quench titration using scFv purified by thec-myc tag (ref.4). Ideally, the affinity for the phOx-BSA conjugatewould have been measured directly, or that for phOx-caproic acid, butphOx-GABA was used here to allow comparison with the hybridoma data ofref.18. The affinities of the antibodies for the phOx conjugate, or forphOx-caproic acid are likely to be better than those measured forphOx-GABA.

FIG. 4—Shows the Assembly of Rearranged VH Genes (See Text)

Methods

A synthetic oligonucleotide SYNLIB1 (see Table IV) introduced aD-segment with a five residue random amino acid sequence, a J-segmentand an XhoI restriction site, to the 3′ end of each of 49 human V_(H)germline segments (Tomlinson et al., supra). The primer was used in thepolymerase chain reaction¹³ with a V_(H) family based back primers(VHBACK) incorporating an NcoI site⁴, HuVH1BackSfi to HuVH6BackSfi. EachV_(H) segment clone (provided as single stranded template in M13 vector)was amplified separately at 94° C. for 1 min, 50° C. for 1 min, and 72°C for 1.5 min, for 25 cycles, on a PHC-3 thermocycler (Techne). Eachamplification was checked by electrophoresis on agarose gel, and similaramounts of DNA from V_(H) segments of the same family were pooled,digested with NcoI and XhoI, and cloned into the vector pHEN1 (ref.14)carrying a rearranged Vlambda3 light chain variable domain (IGLV3S1;ref.12) taken from a scFv fragment binding to BSA⁴.

If, instead of a random oligonucleotide, an oligonucleotide encoding aCDR, eg from a rodent, were used, this would imprint that non-human CDRon the product synthetic human library.

REFERENCES MENTIONED IN EXAMPLE 5

-   1. McCafferty, J., Griffths, A. D., Winter, G. & Chiswell D. J.    (1990). Nature, 348, 552-554.-   2. Mulstein, C. (1990). Proc R Soc Lond Biol, 239, 1-16.-   3. Winter, G. & Milstein, C (1991). Nature, 349, 293-299.-   4. Marks, J. D., et al (1991). J Mol Biol, 222, 581-597.-   5. Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. M. &    Gottesman, K. S. Sequences of proteins of immunological interest (US    Department of Health and Human Services, US Government Printing    Office, 1987).-   6. Matthyssens, G. & Rabbits, T. H. (1980). Proc Natl Acad Sci USA,    77, 6561-6565.-   7. Amit, A. G., Mariuzza, R. A., Phillips, S. E. & Poljak, R. J.    (1986). Science, 233, 747-753.-   8. Alzari, P. M. et al (1990). Embo J, 9, 3807-3814.-   9. Ichihara, Y., Matsuoka, H. & Kurosawa, Y (1988). Embo J, 7,    4141-4150.-   10. Chothia, C. & Lesk, A. M. (1987). J Mol Biol, 196, 901-917.-   11. Chothia, C., et al (1989). Nature, 342, 877-883.-   12. Frippiat, J. P., et al (1990). Nucleic Acids Res, 18, 7134.-   13. Saiki, R. K., et al (1985). Science, 230, 1350-1354.-   14. Hoogenboom, H. R., et al (1991). Nucleic Acids Res, 19,    4133-4137.-   15. Huston, J. S., et al (1988). Proc Natl Acad Sci USA, 85,    5879-5883.-   16. Bird, R. E., et al (1988). Science, 242, 423-426.-   17. Eisen, H. N. (1964). Meth Med Research, 10, 115-121.-   18. Foote, J. & Milstein, C. (1991). Nature, 352, 530-532.-   19. Clackson, T., Hoogenboom, H. R., Griffiths, A. D. & Winter, G    (1991). Nature, 352, 624-628.-   20. Roberts, A. J., et al (1992). Bio/Technoloqy, in press.-   21. Gussow, D. & Clackson, T. (1989). Nucleic Acids Res, 17, 4000.-   22. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). Proc Natl Acad    Sci USA, 74, 5463-5467.-   23. Munro, S. & Pelham, H. R. B. (1986). Cell, 46, 291-300.-   24. Chen, P. P., Liu, M. F., Sinha, S. & Carson, D. A. (1988).    Arthritis Rheum, 31, 1429-1431.-   25. Berman, J. E., et al (1988). Embo J, 7, 727-738.-   26. Matsuda, F., et al (1990). Embo J, 9, 2501-2506.-   27. Sanz, I., et al (1989). Embo J, 8, 3741-3748.-   28. Rath, S., Stanley, C. M. & Steward, M. W. (1988). J Immunol    Methods, 106, 245-249.

EXAMPLE 6

Isolation of Antibody Fragments Specific for Tumour Necrosis Factor-afrom a Germ Line Human Synthetic Library

A clone encoding an antibody fragment specific for tumour necrosisfactor-α was isolated from a germ line human synthetic library Thislibrary was prepared as described in example 5, except that theoligonucleotide SYNLIB2 was used in place of SYNLIB1, so that a 5 aminoacid V_(H) CDR3 was generated. The library was panned against tumournecrosis factor-α, as described in example 1 for the library derivedfrom unimmunised humans. After four rounds of panning a phage antibody(and corresponding soluble fragment) was isolated with binding activityto TNF. The V_(H) region of the scFv fragment (αTNF-10) was derived fromthe VH segment DP-45 (Tomlinson et al, 1992, supra). The hapten bindingclones αNIP-6, αNIP-12, αOx-15 and αOx-18 are also derived from thissegment, although each of these fragments were nevertheless specific forbinding to hapten or TNF. This indicates that antigen binding sites withentirely different specificities can be created on the same antibodyframework by substitution of CDR3 alone. Binding to non-specificantigens was assessed by ELISA as described in example 1.

EXAMPLE 7

Isolation of Single Chain Fv Fragments Binding to Human Thyroglobulinand a Human Monoclonal Antibody from a Germ Line Human Synthetic LibraryContaining VH CDR3 Sequences of Different Lengths

A germ line human synthetic single chain Fv fragment library wasprepared in an analagous manner to the library in Example 5, to includegerm line VH segments and synthetic DH and JH regions, generating VHCDR3 regions of between 4 and 12 amino acids. A single germ linerearranged light chain was provided. This phage library has been used asa source of antibody fragments with anti-human specificities.

Fifty germ line gene VH segments (Tomlinson et al, 1991 supra, as inExample 5) were amplified with oligonucleotides to introduce acompletely randomised CDR3 varying in length from 4 to 12 residues. In afirst PCR-reaction, each gene was amplified with its family specificVHBACK-primer (one of VH1BACKSfi to VH6BACKSfi; Marks et al, 1991 supra;WO92/01047) at the 5′ end, and, annealing at the 3′ end, one of each ofthe oligonucleotides of the series SYNLIB4-SYNLIB12 (Table IV). The PCRcontained 2.5 pmol of each of the appropriate pair of oligonucleotidesper 50 μl reaction mix containing 250 μM dNTPs, 10 mM KCl, 10 mM(NH4)₂SO₄, 20 mM TrisHCl (pH8.8), 2 mM MgCl2, 100 μg/ml BSA and 1 μl (1unit) of Taq DNA polymerase (Cetus). The template was 1 μl of abacterial stock of E. coli infected with a M13 phage clone encoding theappropriate germ line V gene. The amplification cycle was 94° C. for 1min, 55° C. for 1 min and 72° C. for 1.5 min. After 25 cycles, 30 pmolof the same VHBACK oligonucleotide and 30pmol of JHSAL (Table IV) wasadded, and the PCR continued for 15 cycles, introducing a SalI cloningsite at the 3′ end of the VH-gene. After verifying that a band of theappropriate size was seen on agarose gel electrophoresis, the PCRproducts of all amplifications done with the same SYNLIB primer werecollected, cut with NcoI and SalI, and cloned into NcoI-XhoI-cut pHEN1-V3 (pHEN1 containing cloned IGLV3S1) as in Example 5. In this way, 9libraries (each with one particular CDR3 length) were made, eachcontaining between 5×10⁶ and 5×10⁷ clones.

Selection

Phage was prepared from the nine different libraries by rescue withVCS-M13 as described in Example 3. Phage from the nine individuallibraries was mixed to give one large library and subjected to panningon one of each of 2 antigens: Immunosorp tubes were coated with OAK3(human anti-Rhesus D antibody, IgG3, k) overnight in carbonate buffer(0.1 M NaHCO₃, pH 9.6 at 100 μg/ml) or human thyroglobulin (coated at100 μg/ml in PBS). Selections were performed as in Example 3.

Screening

ELISA was performed as described in Hoogenboom et al, 1991 supra. ELISAplates were coated overnight with OAK3 at 100 μg/ml in PBS at roomtemperature or with human thyroglobulin at 100 μg/ml at roomtemperature.

Results

After four rounds of selection on OAK3-coated tubes, eluted phage wasused to infect HB2151, and soluble scFv fragments analysed for bindingby ELISA. 59/96 clones were scored positive in the OAK3 ELISA.

The germ line human synthetic library was also subjected to: 5 rounds ofselection on human thyroglobulin coated tubes, 80/96 clones were foundto be positive in a phage ELISA of individual clones rescued withVCS-M13.

Two of each of the positive clones were analysed in ELISA for bindingagainst a range of antigens (OAK3, human thyroglobulin, phOx-BSA,NIP-BSA, BSA, ovalbumin, chymotrypsinogen-A, streptavidin, cytochrome c,KLH, turkey egg-white lysozyme). The two OAK-3-binding clones (assoluble scFv fragments) both gave signals approximately 3-fold higherthan background in ELISA on OAK3. The two thyroglobulin binding clones(as scFv fragments displayed on phage) both gave signals approximately5-fold higher than background in thyroglobulin-ELISA. All the cloneswere found to be highly specific for the antigen against which they hadbeen selected. By hybridisation to family-specific primers (J. D. Markset al, Eur. J. Immunol. 21 985-991 1991), the VH segment of all fourclones was identified to be of the VH3 family. The CDR3 length of eachclone was analysed by amplifying the CDR3 with oligonucleotides CDRFORand CDRBACK (Table IV), and analysing the product on a 8% polyacrylamidegel. For the two OAK3-binding clones, we found a length of 4 or 7 aminoacid residues, while the thyroglobulin binding clones both use a CDR3length of 10 residues.

Hence, antibody scFv fragments binding to a human monoclonal antibodyand a human self antigen have been isolated from a human germ linesynthetic library.

EXAMPLE 8

Isolation of Antibody Fragments Triggering the Activity of theInterleukin-1 Receptor

The library of single chain Fv fragments derived from an unimmunisedhuman that was described in Example 1 is used to select antibodies whichwill trigger the activity of the interleukin-1 receptor. Antibodyfragments are first isolated which bind to the soluble external domainof the interleukin-1 receptor (IL-1R) of T cells. Antibody clones thatare thus identified are then analysed in assays for interleukin-1 typebiological activity. The IL-1R on murine and human T cells is a highlyhomologous 80 kD cell surface glycoprotein which binds bothinterleukin-1α and interleukin-1β. A cDNA clone encoding the N terminal316 amino acids of the murine receptor external domain has beenexpressed in HeLa cells (S. K. Dower et al. J. Immunol. 142 4314-43201989). The soluble IL1-R molecule thus expressed has been purified andshows binding properties indistinguishable from the full length IL-1Rmolecule, a complex being formed between a single soluble IL1-R moleculeand IL-1. This soluble receptor molecule binds to human interleukin-1.The human T cell interleukin 1 receptor has been cloned and sequenced byJ. E. Sims et al (Proc. Natl. Acad. Sci. USA 86 8946-8950, 1989). Thesoluble external domain of the human IL1 receptor, amino acids 1 to 316,is expressed in HeLa cells and purified as described for the murinereceptor.

The rescued unimmunised human library is first selected against therecombinant human soluble IL-1 receptor, corresponding to the externaldomain of the IL-1 receptor. Immunotubes are coated with the solubleIL-1 receptor as described in Example 1 at 10 μg/ml and panning isperformed as described in Example 1 for a total of four rounds ofaffinity selection.

Clones binding to soluble IL-1 receptor are characterised by ELISA usingmicrotitre plates coated with recombinant soluble IL-1 receptor at 10μg/ml as described for TNF-α in Example 3. Antibody fragments showingsignificant ELISA signals with soluble IL-1 receptor but not withnon-specific antigens are when chosen for further study.

Antibody clones isolated in this way are then expressed as soluble scFvfragments in E. Coli and purified as described in Example 4 by mAb 9E10affinity chromatography. Binding to human receptors is assessed usingbinding of ¹²⁵I-labelled antibody fragment to human fibroblast cell lineTIG-1 expressing the interleukin-1 receptor basically as described by T.Takii et al (Eur. J. Immunol. 22 1221-1227 1992) for determining theaffinity of ¹²⁵I-IL1α for the receptor on these cell lines. The purifiedantibody fragments that show receptor binding are used in a biologicalscreening assay using human epithelial cells to examine them forstimulation of synthesis of prostacyclin (PGI2) and platelet activatingfactor (PAF) as described by E. Dejana et al (Blood 69 695-699, 1987).These studies will identify antibody fragments which have an antiselfspecificity against IL-1 receptor which triggers receptor activity. Theactivity can be quantified relative to human interleukin-1α using astandard bioassay for IL-1α for example proliferation of the D10S helperT cell line using ³H-thymidine incorporation (S. F. Orencole and C. A.Dinarello Cytokine 1 14-22 1989) or a conversion proliferation assay asdescribed by A. J. Gearing et al (J. Immunol. Methods 99 7-11, 1987).TABLE I Frequency of binding clones isolated from the unimmunised scFvlibrary after selection No. of Rounds of selection unique Antigen 1 2 34 5 clones Thyroglobulin — — 18/40 — — 12 (bovine) Thyroglobulin — —10/40 — — 4 (human): selected on bovine Fog1 (human IgG1, — — — 94/96 —4 k antibody) TNFα (human) — 122/1920  83/192 92/96 — 7 CEA (human) — — 0/96  1/96 2/96 1 MUC1 (human): — — —  0/96 2/96 1 selected withpeptide rsCD4 (human) — — — — 8/96 1

The ratios indicate the frequency of binding clones after each round ofselection. Phagemids were rescued with M13DgIII helper phage, except forthe CEA, MUC1 and rsCD4 selections, where VCS-M13 helper phage was used.TABLE II V-gene family, germline derivation and extent of somatichypermutation of several antigen-specific scFv fragments isolated fromthe unimmunised library Germline gene of Differences closest fromgermline nucleotide Amino- scFv Family sequence Nucleotide acid HEAVYCHAINS αThy-23 VH3 DP-47 13 8 αThy-29 VH1 DP-14 0 0 αThy-32 VH3 DP-31 52 αThy-33 VH3 DP-49 32 19 αFOG1-A3 VH3 DP-54 7 3 αFOG1-A4 VH3 DP-46 7 7αFOG1-H6 VH3 DP-51 10 4 αF0G1-G8^(a)) VH4 DP-63 (FR1) 2 0 VH5 DP-73(CDR1 15 7 to FR3) αTNF-A1 VH3 DP-50 9 6 αTNF-E1 VH3 DP-46 14 6 αTNF-E7VH1 DP-10 0 0 αTNF-H9G1 VH1 DP-4 1 1 αCEA4-8A VH1 DP-14 1 0 αMUC1-1^(a))VH1 VI-2 (FR1 2 0 to CDR2) VH1 DP-25 (FR3) 0 0 αCD4-74 VH5 DP-73 13 8LIGHT CHAINS αThy-23 Vk1 L8 20 9 αThy-29 V 3 IGLV3S1 0 0 αThy-32 V 1IGLV1S2 1 1 αThy-33^(a)) Vk1 L12 (FR1 & CDR1) 6 3 Vk4 B3 (FR2 to FR3) 55 αFOG1-A3 V 2 VL2.1 16 9 αFOG1-A4 Vk1 O4 25 12 αFOG1-H6 Vk1 L5 36 17αFOG1-G8 Vk1 L8 27 14 αTNF-A1 Vk1 L11 12 8 αTNF-E1 Vk1 L5 5 5 αTNF-E7Vk1 L11 17 8 αTNF-H9G1 V 1 IGLV1S2 18 9 αCEA4-8A Vk1 O2 4 0 αMUC1-1 V 2VL2.1 18 12 αCD4-74 V 1 Humlv1L1 23 17

References for all the heavy chain germline genes can be found inTomlinson et al. (1992). The references for the light chains are VL2.1(Brockly et al. 1989); IGLV1S2 (Bernard et al. 1990); IGLV3S1 (Frippiatet al. 1990); L8(Vd) and L5(Vb) (Pech et al., 1984); L12(HK102) (Bentleyand Rabbits, 1980); B3(VKIV) (Klobeck et al., 1985); 02 and 04 (Pargentet al., 1991); L11 (Scott et al., 1991); Humlv1L1 (Daley et al., 1992).Alternative names are given in parenthesis.

a) These genes appear to have been created by cross-overs between twoV-genes during PCR amplification and therefore matches have beendetermined using the two putative germline segments: FR, framework; CDR,complementarity-determining region.

-   Bentley, D. L. and Rabbits, T. H. (1980) Nature, 288, 730-3.-   Bernard, F., Chuchana, P., Frippiat, J. P., Buluwela, L. and    Lefranc, M. P. (1990) Nucleic Acids Res, 18, 7139.-   Brockly, F., Alexandre, D., Chuchana, P., Huck, S., Lefranc, G. and    Lefranc, M. P. (1989) Nucleic Acids Res, 17, 3976.-   Frippiat, J. P., Chuchana, P., Bernard, F., Buluwela, L.,    Lefranc, G. and Lefranc, M. P. (1990) Nucleic Acids Res, 18, 7134.-   Klobeck, H. G. Bornkamm, G. W., Combriato, G., Mocikat, R.,    Pohlenz, H. D. and Zachau, H. G. (1985) Nucleic Acids Res, 13,    6515-29.-   Pargent, W., Meindl, A., Thiebe, R., Mitzel, S. and    Zachau, H. G. (1991) Eur J Immunol, 21, 1821-7.-   Pech, M., Jaenichen, H. R., Pohlenz, H. D., Neumaier, P. S.,    Klobeck, H. G. and Zachau, (1984) J Mol Biol, 176, 189-204.-   Scott, M. G., Crimmins, D. L., McCourt, D. W., Chung, G.,    Schable, K. F., Thiebe, R., Quenzel, E. M., Zachau, H. G. and    Nahm, M. H. (1991) J Immunol, 47, 4007-13.

Tomlinson, I. M. Walter, G., Marks, J. D., Llewelyn, M. B. and Winter,G. (1992) J. Mol. Biol., 227, in press. TABLE III Affinities andkinetics of antigen binding by monomeric and dimeric scFv fragmentsk_(on) ^(b)) k_(off) ^(b)) K_(a) = k_(on)/k_(off) K_(a) by FQ^(c)) orImmobilised (BIAcore) (BIAcore) (BIAcore) inhibition^(d)) scFv(M/D)^(a)) species M⁻¹ s⁻¹/10⁴ s⁻¹/10⁻² M⁻¹/10⁶ M⁻¹/10⁶ αTNF-E7 D HumanTNFα  9.0 (±1.2)  1.4 (0.054) 6.4 ND αFOG1-H6 D Fog-1 (direct) 22.2(±0.4) 1.8 (0.23) 12.3 ND αFOG1-H6 D Fog-1 (via RAMIgG1) 22.1 (±1.9) 2.4 (0.045) 9.3 ND αFOG1-H6 D αFOG1-H6 scFv  104 (±2.4) ND^(c)) ND NDαFOG1-H6 M + D (Measured by inhibition) ND ND ND 0.3^(d)) αFOG1-A3 M + D(Measured by inhibition) ND ND ND 0.6^(d)) αThy-29 D Human Thyroglobulin 6.6 (±1.2) 0.46 (0.063) 14.3 ND αThy-29 M Human Thyroglobulin ND 2.0(0.37) ND ND αTEL9 M Turkey Egg Lysozyme 39.2 (±2.6) 1.0 (0.97) 39.211.6^(c))^(a))M, monomeric fraction; D, dimeric fraction^(b))Numbers in brackets are standard deviations^(c))FQ, fluorescence quench titration^(d))Calculated from the extent of inhibition of ¹²⁵l-Fog-1 binding tothe Rh D antigen^(e))Not determined because the dissociation curves were very badly bent

TABLE IV Oligonucleotides used SYNLIB1: (SEQ ID NO.: 1) 5′GCC TCC ACCTCT CGA GAC GGT GAC CAG GGT ACC TTG GCC CCA ATA GTC AAA (A/CNN)5 TCT TGCACA GTA ATA CAC GGC CGT GTC-3′ SYNLIB2: (SEQ ID NO.: 2) 5′GCC TCC ACCTCT CGA GAC GGT GAC CAG GGT ACC TTG GCC CCA (A/CNN)5 TCT TGC ACA GTA ATACAC GGC CGT GTG-3′ SYNLIB4: (SEQ ID NO.: 3) 5′-GAC CAG GGT ACC TTG GCCCCA ((A/C)NN)4 TCT TGC ACA GTA ATA CAC GGC CGT GTC-3′ SYNLIB5: (SEQ IDNO.: 4) 5′-GAC CAG GGT ACC TTG GCC CCA ((A/C)NN)5 TCT TGC ACA GTA ATACAC GGC CGT GTC-3′ SYNLIB6: (SEQ ID NO.: 5) 5′-GAC CAG GGT ACC TTG GCCCCA ((A/C)NN)6 TCT TGC ACA GTA ATA CAC GGC CGT GTC-3′ SYNLIB7: (SEQ IDNO.: 6) 5′-GAC CAG GGT ACC TTG GCC CCA ((A/C)NN)7 TCT TGC ACA GTA ATACAC GGC CGT GTC-3′ SYNLIB8: (SEQ ID NO.: 7) 5′-GAC CAG GGT ACC TTG GCCCCA ((A/C)NN)8 TCT TGC ACA GTA ATA CAC GGC CGT GTC-3′ SYNLIB9: (SEQ IDNO.: 8) 5′-GAC CAG GGT ACC TTG GCC CCA ((A/C)NN)9 TCT TGC ACA GTA ATACAC GGC CGT GTC-3′ SYNLIB10: (SEQ ID NO.: 9) 5′-GAC CAG GGT ACC TTG GCCCCA ((A/C)NN)10 TCT TGC ACA GTA ATA CAC GGC CGT GTC-3′ SYNLIB11: (SEQ IDNO.: 10) 5′-GAC CAG GGT ACC TTG GCC CCA ((A/C)NN)11 TCT TGC ACA GTA ATACAC GGC CGT GTC-3′ SYNLIB12: (SEQ ID NO.: 11) 5′-GAC CAG GGT ACC TTG GCCCCA ((A/C)NN)12 TCT TGC ACA GTA ATA CAC GGC CGT GTC-3′ JHSAL: (SEQ IDNO.: 12) 5′- GCC TGA ACC GCC TCC ACC AGT CGA CAC GGT GAC CAG GGT ACC TTGGCC CCA-3′ CDRFOR: (SEQ ID NO.: 13) 5′- CAG GGT ACC TTG GCC CCA-3′CDRBACK: (SEQ ID NO.: 14) 5′- GTG TAT TAC TGT GCA AGA-3′ Human VH BackPrimers HuVH1aBACKSfi (SEQ ID NO.: 15) 5′-GTC CTC GCA ACT GCG GCC CAGCCG GCC ATG GCC CAG GTG CAG CTG GTG CAG TCT GG-3′ HuVH2aBACKSfi (SEQ IDNO.: 16) 5′-GTC CTC GCA ACT GCG GCC CAG CCG GCC ATG GCC CAG GTC AAC TTAAGG GAG TCT GG-3′ HuVH3aBACKSfi (SEQ ID NO.: 17) 5′-GTC CTC GCA ACT GCGGCC CAG CCG GCC ATG GCC GAG GTG CAG CTG GTG GAG TCT GG-3′ HuVH4aBACKSfi(SEQ ID NO.: 18) 5′-GTC CTC GCA ACT GCG GCC CAG CCG GCC ATG GCC CAG GTGCAG CTG CAG GAG TCG GG-3′ HuVH5aBACKSfi (SEQ ID NO.: 19) 5′-GTC CTC GCAACT GCG GCC CAG CCG GCC ATG GCC CAG GTG CAG CTG TTG CAG TCT GC-3′HuVH6aBACKSfi (SEQ ID NO.: 20) 5′-GTC CTC GCA ACT GCG GCC CAG CCG GCCATG GCC CAG GTA CAG CTG CAG CAG TCA GG-3′

1. A method of obtaining a member of a specific binding pair (sbpmember), which sbp member has an antigen binding site with bindingspecificity for an antigen which is a self antigen of a species ofmammal, wherein the sbp member is a VH domain of an antibody, the methodcomprising: (a) providing a library of replicable genetic displaypackages (rgdps), each rgdp displaying at its surface an sbp member, andeach rgdp containing nucleic acid with sequence derived from saidspecies of mammal and encoding the sbp member displayed at the surfaceof that rgdp; (b) selecting, by binding with said self antigen, one ormore sbp members with binding specificity for said self antigen.
 2. Amethod of obtaining a member of a specific binding pair (sbp member),which sbp member has an antigen binding site with binding specificityfor an antigen which is a self antigen of a species of mammal, whereinthe sbp member is a VL domain of an antibody, the method comprising: (a)providing a library of replicable genetic display packages (rgdps), eachrgdp displaying at its surface an sbp member, and each rgdp containingnucleic acid with sequence derived from said species of mammal andencoding the sbp member displayed at the surface of that rgdp; (b)selecting, by binding with said self antigen, one or more sbp memberswith binding specificity for said self antigen.
 3. The method accordingto claim 1 or claim 2 wherein the nucleic acid is derived fromrearranged V genes of an unimmunised mammal.
 4. The method according toclaim 1 or claim 2 wherein the nucleic acid is derived from a libraryprepared by artificial or synthetic recombination of V gene sequences.5. The method according to claim 4 wherein the library is derived fromgerm line V-gene sequences.
 6. The method according to claim 1 whereinsaid species of mammal is human.
 7. The method according to claim 1 orclaim 2 wherein sbp members selected in (b) displayed at the surface ofrgdps are selected or screened to provide an individual rgdp displayingan sbp member or a mixed population of said rgdps, with each rgdpcontaining nucleic acid encoding the sbp member which is displayed atits surface.
 8. The method claim 7 wherein nucleic acid which encodes aselected or screened sbp member and which is derived from a rgdp whichdisplays at its surface a selected or screened sbp member is used toexpress an sbp member or a fragment or derivative thereof in arecombinant host organism.
 9. The method according to claim 8 whereinnucleic acid from one or more rgdps is taken and used to provideencoding nucleic acid in a further method to obtain an individual sbpmember or a mixed population of sbp members, or encoding nucleic acidtherefor.
 10. The method according to claim 8 wherein the expression endproduct is modified to produce a derivative thereof.
 11. The methodaccording to claim 8 wherein the expression end product or derivativethereof is used to prepare a therapeutic or prophylactic medicament or adiagnostic product.
 12. The method according to claim 1 or claim 2wherein the self antigen is Tumour Necrosis Factor Alpha (TNFα).
 13. Themethod according to claim 1 or claim 2 wherein the self antigen isthyroglobulin.
 14. The method according to claim 1 or claim 2 whereinthe self antigen is a receptor.
 15. The method according to claim 1 orclaim 2 wherein the self antigen is mucin.
 16. The method according toclaim 1 or claim 2 wherein the self antigen is carcinoembryonic antigen(CEA).
 17. The method according to claim 1 or claim 2 wherein the selfantigen is CD4.
 18. An isolated VH domain of an antibody of a species ofmammal, wherein the VH domain has binding specificity for an antigenwhich is a self antigen of the species of mammal.
 19. The isolated VHdomain according to claim 18, wherein said species of mammal is human.20. An isolated VL domain of an antibody of a species of mammal, whereinthe VL domain has binding specificity for an antigen which is a selfantigen of the species of mammal.
 21. The isolated VL domain accordingto claim 20, wherein said species of mammal is human.
 22. The isolatedVH domain according to claim 18 or isolated VL domain according to claim20, wherein the self antigen is Tumour Necrosis Factor Alpha (TNFα). 23.The isolated VH domain according to claim 18 or isolated VL domainaccording to claim 20, wherein the self antigen is thyroglobulin. 24.The isolated VH domain according to claim 18 or isolated VL domainaccording to claim 20, wherein the self antigen is a receptor.
 25. Theisolated VH domain according to claim 18 or isolated VL domain accordingto claim 20, wherein the self antigen is mucin.
 26. The isolated VHdomain according to claim 18 or isolated VL domain according to claim20, wherein the self antigen is carcinoembryonic antigen (CEA).
 27. Theisolated VH domain according to claim 18 or isolated VL domain accordingto claim 20, wherein the self antigen is CD4.
 28. A replicable geneticdisplay package (rgdp) displaying a VH domain of an antibody of aspecies of mammal or a VL domain of an antibody of a species of mammal,wherein the VH domain or the VL domain has binding specificity for anantigen which is a self antigen of the species of mammal.
 29. Thereplicable genetic display package of claim 28 wherein said species ofmammal is human.
 30. A medicament comprising the isolated VH domain ofclaim 18 or isolated VL domain according to claim
 20. 31. A method oftreatment of disease in a human, comprising administering to the humanthe isolated VH domain of claim 19 or isolated VL domain according toclaim 21.